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- EMDB-10180: mt-SSU assemblosome of Trypanosoma brucei -

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Basic information

Entry
Database: EMDB / ID: EMD-10180
Titlemt-SSU assemblosome of Trypanosoma brucei
Map data
Samplemt-SSU assemblosome:
uS5m / bS6m / uS8m / uS11m / uS15m / bS16m / uS17m / bS18m / mS22 / mS23 ...uS5m / bS6m / uS8m / uS11m / uS15m / bS16m / uS17m / bS18m / mS22 / mS23 / mS26 / mS34 / mS38 / mS41 / mS51 (KRIPP1) / mS56 / mS59 / mS62 (KRIPP14) / mS63 (KRIPP16) / mS65 / mS68 / mS73 / mt-SAF2 (KRIPP2) / mt-SAF3 / mt-SAF5 / mt-SAF6 / mt-SAF7 (KRIPP10) / mt-SAF8 / mt-SAF9 / mt-SAF10 / mt-SAF11 / mt-SAF13 / mt-SAF18 / mt-SAF21 / mt-SAF22 (KRIPP17) / mt-SAF23 / mt-SAF24 / mt-SAF26 / mt-SAF27 (KRIPP11) / mt-SAF28 / mt-SAF29 / mt-SAF30 / mt-SAF31 / mt-SAF32 / mt-SAF33 / UNK-A / UNK-B, UNK-k / UNK-C / UNK-D, UNK-M, UNK-Q, UNK-f / UNK-E, UNK-P / UNK-F, UNK-m / UNK-G / UNK-H / UNK-I, UNK-N / UNK-J / UNK-K / UNK-L / UNK-O / UNK-Y / nucleic-acidNucleic acid / mS3m / uS9m / uS10m / uS14m / uS19m / mS29 / mS33 / mS35 / mS49 / mS50 / mS52 / mS53 / mS54 / mS55 (KRIPP8) / mS57 / mS58 / mS67 / mS69 / mS70 / mS71 / mS72 / mt-SAF1 (RSM22) / mt-SAF4 / mt-SAF12 (KRIPP18) / mt-SAF14 / mt-SAF15 / mt-SAF16 / mt-SAF17 / mt-SAF19 / mt-SAF20 / mt-SAF25 / mt-SAF34 / UNK-a / UNK-b / UNK-c / UNK-d / UNK-e / UNK-g / UNK-h / UNK-i / UNK-j / UNK-l / UNK-x / (ligand) x 7
Function / homology
Function and homology information


rRNA (cytosine-N4-)-methyltransferase activity / modulation of development of symbiont involved in interaction with host / mitochondrial mRNA editing complex / RNA polyadenylation / mitochondrial RNA processing / ATP-activated inward rectifier potassium channel activity / kinetoplast / mitochondrial ribosome binding / positive regulation of mitochondrial translation / translation activator activity ...rRNA (cytosine-N4-)-methyltransferase activity / modulation of development of symbiont involved in interaction with host / mitochondrial mRNA editing complex / RNA polyadenylation / mitochondrial RNA processing / ATP-activated inward rectifier potassium channel activity / kinetoplast / mitochondrial ribosome binding / positive regulation of mitochondrial translation / translation activator activity / nuclear lumen / mitochondrial small ribosomal subunit / rRNA base methylation / mitochondrial respiratory chain complex I / acyl binding / acyl carrier activity / ciliary plasm / mRNA stabilization / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transport / protein homooligomerization / Transferases; Transferring one-carbon groups; Methyltransferases / fatty acid biosynthetic process / methyltransferase activity / methylation / structural constituent of ribosome / mitochondrial matrix / translation / mRNA binding / mitochondrion / RNA binding / membrane / cytosol / cytoplasm
S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / Tetratricopeptide-like helical domain superfamily / Rhodanese-like domain / Pentatricopeptide repeat / Ribosomal RNA small subunit methyltransferase H / Potassium channel tetramerisation-type BTB domain / Phosphotyrosine protein phosphatase I / Acyl carrier protein (ACP) / Ribosomal protein S16 domain superfamily / Mitochondrial glycoprotein ...S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / Tetratricopeptide-like helical domain superfamily / Rhodanese-like domain / Pentatricopeptide repeat / Ribosomal RNA small subunit methyltransferase H / Potassium channel tetramerisation-type BTB domain / Phosphotyrosine protein phosphatase I / Acyl carrier protein (ACP) / Ribosomal protein S16 domain superfamily / Mitochondrial glycoprotein / Phosphopantetheine attachment site / S15/NS1, RNA-binding / Probable Zinc-ribbon domain / Phosphopantetheine binding ACP domain / SKP1/BTB/POZ domain superfamily / T-cell activation inhibitor, mitochondrial / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S9 / Domain of unknown function DUF4460 / S-adenosyl-L-methionine-dependent methyltransferase / Phosphotyrosine protein phosphatase I superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Thioredoxin-like superfamily / Ribosomal protein Rsm22-like / Mitochondrial glycoprotein superfamily / ACP-like superfamily / IGR protein motif / Rhodanese-like domain superfamily / Ribosomal protein S11 superfamily / Protein Fyv4 / Ribosomal protein S23/S29, mitochondrial / Ribosomal protein S5 domain 2-type fold
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / S-adenosyl-methyltransferase mraW-like protein, putative / Uncharacterized protein / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Uncharacterized protein ...Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / S-adenosyl-methyltransferase mraW-like protein, putative / Uncharacterized protein / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / DUF4379 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Rhodanese domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Potassium voltage-gated channel, putative / DUF4460 domain-containing protein / Uncharacterized protein / Protein FYV4, mitochondrial / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / LMWPc domain-containing protein / Uncharacterized protein
Biological speciesTrypanosoma brucei brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSaurer M / Ramrath DJF / Niemann M / Calderaro S / Prange C / Mattei S / Scaiola A / Leitner A / Bieri P / Horn EK ...Saurer M / Ramrath DJF / Niemann M / Calderaro S / Prange C / Mattei S / Scaiola A / Leitner A / Bieri P / Horn EK / Leibundgut M / Boehringer D / Schneider A / Ban N
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Science / Year: 2019
Title: Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery.
Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut ...Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut / Daniel Boehringer / André Schneider / Nenad Ban /
Abstract: Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome ...Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria.
Validation ReportPDB-ID: 6sgb

SummaryFull reportAbout validation report
History
DepositionAug 3, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateSep 25, 2019-
Current statusSep 25, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sgb
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10180.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 444.8 Å
1.39 Å/pix.
x 320 pix.
= 444.8 Å
1.39 Å/pix.
x 320 pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.28488272 - 0.61338395
Average (Standard dev.)0.0024740428 (±0.020873765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin565656
Dimensions320320320
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS565656
NC/NR/NS320320320
D min/max/mean-0.2850.6130.002

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Supplemental data

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Sample components

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Entire mt-SSU assemblosome

EntireName: mt-SSU assemblosome / Number of components: 111

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Component #1: protein, mt-SSU assemblosome

ProteinName: mt-SSU assemblosome / Recombinant expression: No
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #2: protein, uS5m

ProteinName: uS5m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.147355 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #3: protein, bS6m

ProteinName: bS6m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.861543 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #4: protein, uS8m

ProteinName: uS8m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.766459 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #5: protein, uS11m

ProteinName: uS11m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.953965 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #6: protein, uS15m

ProteinName: uS15m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.401191 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #7: protein, bS16m

ProteinName: bS16m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.077805 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #8: protein, uS17m

ProteinName: uS17m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence; C-terminal PTP-tag
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.012414 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #9: protein, bS18m

ProteinName: bS18m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.988691 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #10: protein, mS22

ProteinName: mS22
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 73.064141 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #11: protein, mS23

ProteinName: mS23
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.358805 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #12: protein, mS26

ProteinName: mS26
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.136684 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #13: protein, mS34

ProteinName: mS34
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.72818 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #14: protein, mS38

ProteinName: mS38
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.2406 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #15: protein, mS41

ProteinName: mS41
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.421469 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #16: protein, mS51 (KRIPP1)

ProteinName: mS51 (KRIPP1)
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 95.080992 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #17: protein, mS56

ProteinName: mS56
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.306836 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #18: protein, mS59

ProteinName: mS59
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.395676 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #19: protein, mS62 (KRIPP14)

ProteinName: mS62 (KRIPP14)
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.0681 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #20: protein, mS63 (KRIPP16)

ProteinName: mS63 (KRIPP16)
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.922178 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #21: protein, mS65

ProteinName: mS65
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.617381 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #22: protein, mS68

ProteinName: mS68 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.472807 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #23: protein, mS73

ProteinName: mS73 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.360885 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #24: protein, mt-SAF2 (KRIPP2)

ProteinName: mt-SAF2 (KRIPP2) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 116.189547 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #25: protein, mt-SAF3

ProteinName: mt-SAF3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 106.621727 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #26: protein, mt-SAF5

ProteinName: mt-SAF5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.949414 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #27: protein, mt-SAF6

ProteinName: mt-SAF6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 76.781398 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #28: protein, mt-SAF7 (KRIPP10)

ProteinName: mt-SAF7 (KRIPP10) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 76.675156 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #29: protein, mt-SAF8

ProteinName: mt-SAF8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 76.72518 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #30: protein, mt-SAF9

ProteinName: mt-SAF9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.781789 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #31: protein, mt-SAF10

ProteinName: mt-SAF10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.306758 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #32: protein, mt-SAF11

ProteinName: mt-SAF11 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 64.916957 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #33: protein, mt-SAF13

ProteinName: mt-SAF13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.690703 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #34: protein, mt-SAF18

ProteinName: mt-SAF18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.508039 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #35: protein, mt-SAF21

ProteinName: mt-SAF21 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 39.610793 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #36: protein, mt-SAF22 (KRIPP17)

ProteinName: mt-SAF22 (KRIPP17) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.132621 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #37: protein, mt-SAF23

ProteinName: mt-SAF23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.240164 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #38: protein, mt-SAF24

ProteinName: mt-SAF24 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 34.648047 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #39: protein, mt-SAF26

ProteinName: mt-SAF26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.538557 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #40: protein, mt-SAF27 (KRIPP11)

ProteinName: mt-SAF27 (KRIPP11) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.936748 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #41: protein, mt-SAF28

ProteinName: mt-SAF28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.468707 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #42: protein, mt-SAF29

ProteinName: mt-SAF29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.048514 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #43: protein, mt-SAF30

ProteinName: mt-SAF30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.659756 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #44: protein, mt-SAF31

ProteinName: mt-SAF31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.673535 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #45: protein, mt-SAF32

ProteinName: mt-SAF32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.550807 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #46: protein, mt-SAF33

ProteinName: mt-SAF33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.291121 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #47: protein, UNK-A

ProteinName: UNK-A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.805216 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #48: protein, UNK-B, UNK-k

ProteinName: UNK-B, UNK-k / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.315846 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #49: protein, UNK-C

ProteinName: UNK-C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.869063 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #50: protein, UNK-D, UNK-M, UNK-Q, UNK-f

ProteinName: UNK-D, UNK-M, UNK-Q, UNK-f / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.783958 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #51: protein, UNK-E, UNK-P

ProteinName: UNK-E, UNK-P / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 3.847734 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #52: protein, UNK-F, UNK-m

ProteinName: UNK-F, UNK-m / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.954168 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #53: protein, UNK-G

ProteinName: UNK-G / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.464797 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #54: protein, UNK-H

ProteinName: UNK-H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443539 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #55: protein, UNK-I, UNK-N

ProteinName: UNK-I, UNK-N / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.698854 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #56: protein, UNK-J

ProteinName: UNK-J / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.379692 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #57: protein, UNK-K

ProteinName: UNK-K / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.060531 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #58: protein, UNK-L

ProteinName: UNK-L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.890321 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #59: protein, UNK-O

ProteinName: UNK-O / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.571161 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #60: protein, UNK-Y

ProteinName: UNK-Y / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.847105 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #61: nucleic-acid, 9S rRNA

nucleic acidName: 9S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UAAAUUAUGG UCAAUUGUUA GUAUUCAUAU UAAUUUUUUU AAAUGUUUUA UCAUUUUAUA AAGGUUUAUU UUUGAAAGAU UUUUUGUAUA AAAUUUUAGG AAUAGUUAAU AAUAAUUUAU AAUUUUGAUU AGAUUGUUUU GUUAAUGCUA UUAGAUGGGU GUGGAAAAAU ...Sequence:
UAAAUUAUGG UCAAUUGUUA GUAUUCAUAU UAAUUUUUUU AAAUGUUUUA UCAUUUUAUA AAGGUUUAUU UUUGAAAGAU UUUUUGUAUA AAAUUUUAGG AAUAGUUAAU AAUAAUUUAU AAUUUUGAUU AGAUUGUUUU GUUAAUGCUA UUAGAUGGGU GUGGAAAAAU AAAAAAAAUA AUUAAUAUAU AUCAAUAAUA AAUUAAAUUA AUCUAUUAGU CAGAAAUGGA UGCCAGCCGU UGCGGUAAUU UCUAUGCUUU UAAAUAUUAU ACAAUUAUCA UAUUAAAUUG UUAAGUGCUG AUUUAACCAA UAAAAAUAUA AAUAAUUUUU AUUUGUUUUU AAACACCAUU AGGUAUAUGC AAAUAUAAAA UUAUAGUAAU UAUAAAUUAU AUUAUAUUAU AUUUAUUCAU AUAAUUAAUA GGAUAAUAUU UGUAGUUUUU GAUACCAUGA UAAGGAUUAU AAAUUGAAAG UGUUAAUAUC AUAAUCAAAA UUUAUUAUUU AUAUUAAAUA UGUAUGUGUA GAUAAAAUAA GAAAUUAAAA AGGUAUUGUU GCCCACCAAU UUUUAUAAUA AAAAUAACGU GCAGUAAUUA AUAUAUUUAU AAAAAUAUAU UUUUUUUUU(UBD)
MassTheoretical: 198.215203 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #62: protein, mS3m

ProteinName: mS3m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.07094 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #63: protein, uS9m

ProteinName: uS9m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.201016 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #64: protein, uS10m

ProteinName: uS10m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.321055 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #65: protein, uS14m

ProteinName: uS14m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.900014 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #66: protein, uS19m

ProteinName: uS19m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.364604 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #67: protein, mS29

ProteinName: mS29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.048836 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #68: protein, mS33

ProteinName: mS33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.244104 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #69: protein, mS35

ProteinName: mS35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 98.377773 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #70: protein, mS49

ProteinName: mS49 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.234125 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #71: protein, mS50

ProteinName: mS50 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 131.71925 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #72: protein, mS52

ProteinName: mS52 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 84.998234 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #73: protein, mS53

ProteinName: mS53 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 75.310867 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #74: protein, mS54

ProteinName: mS54 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.046031 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #75: protein, mS55 (KRIPP8)

ProteinName: mS55 (KRIPP8) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.67668 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #76: protein, mS57

ProteinName: mS57 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.956293 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #77: protein, mS58

ProteinName: mS58 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.62391 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #78: protein, mS67

ProteinName: mS67 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.096051 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #79: protein, mS69

ProteinName: mS69 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.589732 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #80: protein, mS70

ProteinName: mS70 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.247398 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #81: protein, mS71

ProteinName: mS71 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.093227 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #82: protein, mS72

ProteinName: mS72 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.340352 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #83: protein, mt-SAF1 (RSM22)

ProteinName: mt-SAF1 (RSM22) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 119.799398 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #84: protein, mt-SAF4

ProteinName: mt-SAF4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 91.549312 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #85: protein, mt-SAF12 (KRIPP18)

ProteinName: mt-SAF12 (KRIPP18) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.049215 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #86: protein, mt-SAF14

ProteinName: mt-SAF14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.32082 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #87: protein, mt-SAF15

ProteinName: mt-SAF15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.273867 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #88: protein, mt-SAF16

ProteinName: mt-SAF16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.911414 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #89: protein, mt-SAF17

ProteinName: mt-SAF17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.14759 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #90: protein, mt-SAF19

ProteinName: mt-SAF19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.236418 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #91: protein, mt-SAF20

ProteinName: mt-SAF20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.293855 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #92: protein, mt-SAF25

ProteinName: mt-SAF25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.470537 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #93: protein, mt-SAF34

ProteinName: mt-SAF34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.862911 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #94: protein, UNK-a

ProteinName: UNK-a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.017944 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #95: protein, UNK-b

ProteinName: UNK-b / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.592419 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #96: protein, UNK-c

ProteinName: UNK-c / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.039273 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #97: protein, UNK-d

ProteinName: UNK-d / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.039203 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #98: protein, UNK-e

ProteinName: UNK-e / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.486056 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #99: protein, UNK-g

ProteinName: UNK-g / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.230525 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #100: protein, UNK-h

ProteinName: UNK-h / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.719672 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #101: protein, UNK-i

ProteinName: UNK-i / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.74137 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #102: protein, UNK-j

ProteinName: UNK-j / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.635006 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #103: protein, UNK-l

ProteinName: UNK-l / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.209482 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #104: protein, UNK-x

ProteinName: UNK-x / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.379553 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #105: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #106: ligand, PHOSPHATE ION

LigandName: PHOSPHATE IONPhosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.497105 MDa

+
Component #107: ligand, S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-...

LigandName: S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.496598 kDa

+
Component #108: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #109: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #110: ligand, S-ADENOSYL-L-HOMOCYSTEINE

LigandName: S-ADENOSYL-L-HOMOCYSTEINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.384411 kDa

+
Component #111: ligand, water

LigandName: water / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 278 K / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal), 100719.0 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 104838
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / CTF correction: On the fly in RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Details: Starting models of ribosomal proteins of the T. brucei mitochondrial ribosomal small subunit were taken from PDB 6HIW. Mitchondrial ribosomal small subunit assembly factors were built de novo.
Output model

+
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