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- EMDB-3751: Cryo-EM reconstruction of the Mycobacterium smegmatis 70S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3751
TitleCryo-EM reconstruction of the Mycobacterium smegmatis 70S ribosome
Map data
Sample70S ribosomeRibosome:
(50S ribosomal protein ...) x 31 / (nucleic-acidNucleic acid) x 5 / LSU ribosomal protein L28P / Conserved domain proteinProtein domain / (30S ribosomal protein ...) x 19 / (ligand) x 3
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / ribosome biogenesis / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding ...large ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / ribosome biogenesis / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / metal ion binding
Ribosomal protein S11, bacterial-type / Ribosomal protein L25, beta domain / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L9, N-terminal domain superfamily / 30S ribosomal protein S17 / Ribosomal protein L6, alpha-beta domain ...Ribosomal protein S11, bacterial-type / Ribosomal protein L25, beta domain / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L9, N-terminal domain superfamily / 30S ribosomal protein S17 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein S3, conserved site / Ribosomal protein L9, N-terminal / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S6, conserved site / Ribosomal S11, conserved site / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / K homology domain-like, alpha/beta / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L5, bacterial-type / Domain of unknown function DUF1713 / Ribosomal protein L22/L17 superfamily / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L5, C-terminal / Ribosomal protein S20 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein L15 / Ribosomal protein S19 conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein L10 / Ribosomal protein S14, type Z / Ribosomal protein L25 / Ribosomal protein L4 domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L31 type A / Ribosomal protein L21-like / Ribosomal protein S5, N-terminal / Ribosomal protein L25/L23
30S ribosomal protein S2 / 30S ribosomal protein S13 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / 30S ribosomal protein S9 / Uncharacterized protein / 50S ribosomal protein L28 / 30S ribosomal protein S16 ...30S ribosomal protein S2 / 30S ribosomal protein S13 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / 30S ribosomal protein S9 / Uncharacterized protein / 50S ribosomal protein L28 / 30S ribosomal protein S16 / 50S ribosomal protein L19 / 50S ribosomal protein L21 / 30S ribosomal protein S15 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 30S ribosomal protein S20 / 50S ribosomal protein L27 / 50S ribosomal protein L15 / 50S ribosomal protein L31 / 50S ribosomal protein L25 / 50S ribosomal protein L32 / 50S ribosomal protein L9 / 30S ribosomal protein S18 2 / 50S ribosomal protein L34 / 50S ribosomal protein L28 / 50S ribosomal protein L36 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L30 / 50S ribosomal protein L2 / 30S ribosomal protein S6 / Conserved domain protein / 50S ribosomal protein L33 1 / 50S ribosomal protein L11 / 50S ribosomal protein L10 / 30S ribosomal protein S12 / 30S ribosomal protein S7 / 30S ribosomal protein S10 / 50S ribosomal protein L3 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 30S ribosomal protein S19 / 30S ribosomal protein S5 / 50S ribosomal protein L22 / 30S ribosomal protein S3 / 50S ribosomal protein L16 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L15
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsHentschel J / Burnside C / Mignot I / Leibundgut M / Boehringer D / Ban N
CitationJournal: Cell Rep / Year: 2017
Title: The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Authors: Jendrik Hentschel / Chloe Burnside / Ingrid Mignot / Marc Leibundgut / Daniel Boehringer / Nenad Ban /
Abstract: The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death ...The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 3, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseJul 12, 2017-
UpdateJul 19, 2017-
Current statusJul 19, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5o61
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5o61
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3751.map.gz / Format: CCP4 / Size: 38.4 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 216 pix.
= 300.24 Å
1.39 Å/pix.
x 216 pix.
= 300.24 Å
1.39 Å/pix.
x 216 pix.
= 300.24 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: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.18659295 - 0.43669373
Average (Standard dev.)0.0020679191 (±0.0344998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z300.240300.240300.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.1870.4370.002

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Supplemental data

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Sample components

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Entire 70S ribosome

EntireName: 70S ribosomeRibosome / Number of components: 61

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Component #1: protein, 70S ribosome

ProteinName: 70S ribosomeRibosome / Recombinant expression: No
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #2: protein, 50S ribosomal protein bL37

ProteinName: 50S ribosomal protein bL37 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.841375 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #3: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UAAGUGUUUA AGGGCGCAUG GUGGAUGCCU UGGCACUGGG AGCCGAUGAA GGACGUAGGA GGCUGCGAUA AGCCUCGGGG AGCUGUCAAC CGAGCGUUGA UCCGAGGAUG UCCGAAUGGG GAAACCCGGC ACGAGUGAUG UCGUGUCACC AGGCGCUGAA UAUAUAGGCG ...Sequence:
UAAGUGUUUA AGGGCGCAUG GUGGAUGCCU UGGCACUGGG AGCCGAUGAA GGACGUAGGA GGCUGCGAUA AGCCUCGGGG AGCUGUCAAC CGAGCGUUGA UCCGAGGAUG UCCGAAUGGG GAAACCCGGC ACGAGUGAUG UCGUGUCACC AGGCGCUGAA UAUAUAGGCG UCUGGGGGGA ACGCGGGGAA GUGAAACAUC UCAGUACCCG UAGGAAGAGA AAACAAAAUG UGAUUCCGUG AGUAGUGGCG AGCGAAAGCG GAGGAUGGCU AAACCGUAUG CAUGUGAUAC CGGGUAGGGG UUGUGUGUGC GGGGUUGUGG GACCUAUCUU UCCGGCUCUA CCUGGCUGGA GGGCAGUGAG AAAAUGUUGU GGUUAGCGGA AAUGGCUUGG GAUGGCCUGC CGUAGACGGU GAGAGCCCGG UACGUGAAAA CCCGACGUCU GUCUUGAUGG UGUUCCCGAG UAGCAGCGGG CCCGUGGAAU CUGCUGUGAA UCUGCCGGGA CCACCCGGUA AGCCUGAAUA CUUCCCAGUG ACCGAUAGCG GAUUAGUACC GUGAGGGAAU GGUGAAAAGU ACCCCGGGAG GGGAGUGAAA GAGUACCUGA AACCGUGCGC UUACAAUCCG UCAGAGCCCU CGACGUGUCG UGGGGUGAUG GCGUGCCUUU UGAAGAAUGA GCCUGCGAGU CAGGGACAUG UCGCGAGGUU AACCCGGGUG GGGUAGCCGC AGCGAAAGCG AGUCUGAAUA GGGCGUAUCC ACACAAGAGU GUGUGGUGUA GUGGUGUGUU CUGGACCCGA AGCGGAGUGA UCUACCCAUG GCCAGGGUGA AGCGCGGGUA AGACCGCGUG GAGGCCCGAA CCCACUUAGG UUGAAGACUG AGGGGAUGAG CUGUGGGUAG GGGUGAAAGG CCAAUCAAAC UCCGUGAUAG CUGGUUCUCC CCGAAAUGCA UUUAGGUGCA GCGUCGCAUG UUUCUUGCCG GAGGUAGAGC UACUGGAUGG CCGAUGGGCC CCACAGGGUU ACUGACGUCA GCCAAACUCC GAAUGCCGGU AAGUCCAAGA GUGCGGCAGU GAGACGGCGG GGGAUAAGCU CCGUGCGUCG AGAGGGAAAC AGCCCAGAUC GCCGGCUAAG GCCCCUAAGC GUGUGCUAAG UGGAAAAGGA UGUGCAGUCG CGAAGACAAC CAGGAGGUUG GCUUAGAAGC AGCCACCCUU GAAAGAGUGC GUAAUAGCUC ACUGGUCAAG UGAUUGUGCG CCGAUAAUGU AGCGGGGCUC AAGCACACCG CCGAAGCCGC GGCAGCCAAC GUGUUGGCUG GGUAGGGGAG CGUCCUGCAU CCGGUGAAGC CGCCGAGUGA UCGAGUGGUG GAGGGUGUGG GAGUGAGAAU GCAGGCAUGA GUAGCGAUUA GGCAAGUGAG AACCUUGCCC GCCGAAAGAC CAAGGGUUCC UGGGCCAGGC CAGUCCGCCC AGGGUGAGUC GGGACCUAAG GCGAGGCCGA CAGGCGUAGU CGAUGGACAA CGGGUUGAUA UUCCCGUACC CGUGUAUGUG CGUCCAUGAU GAAUCAGCGG UACUAACCAU CCAAAACCAC CGUGACCGCA CCUUUCGGGG UGUGGCGUUG GUGGGGCUGC AUGGGACCUU CGUUGGUAGU AGUCAAGCGA UGGGGUGACG CAGGAAGGUA GCCGUACCGG UCAGUGGUAA UACCGGGGUA AGCCUGUAGG GAGUCAGAUA GGUAAAUCCG UCUGGCAUAU AUCCUGAGAG GUGAUGCAUA GCCGAGUGAG GCGAAUUCGG UGAUCCUAUG CUGCCGAGAA AAGCCUCUAG CGAGGACAUA CACGGCCCGU ACCCCAAACC AACACAGGUG GUCAGGUAGA GAAUACUAAG GCGUACGAGU GAACUAUGGU UAAGGAACUC GGCAAAAUGC CCCCGUAACU UCGGGAGAAG GGGGACCCAC AUGGCGUGUA AGCCUUUACG GCCCAAGCGU GAGUGGGUGG CACAAACCAG UGAGAAGCGA CUGUUUACUA AAAACACAGG UCCGUGCGAA GUCGCAAGAC GAUGUAUACG GACUGACGCC UGCCCGGUGC UGGAAGGUUA AGAGGACCCG UUAACUCCCU UUGGGGGUGA AGCGGAGAAU UUAAGCCCCA GUAAACGGCG GUGGUAACUA UAACCAUCCU AAGGUAGCGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AACGACUUCU CAACUGUCUC AACCAUAGAC UCGGCGAAAU UGCACUACGA GUAAAGAUGC UCGUUACGCG CGGCAGGACG AAAAGACCCC GGGACCUUCA CUACAACUUG GUAUUGGUGC UCGAUACGGU UUGUGUAGGA UAGGUGGGAG ACUGUGAAGC UCACACGCCA GUGUGGGUGG AGUCGUUGUU GAAAUACCAC UCUGAUCGUA UUGGGCCUCU AACCUCGGAC CGUAUAUCCG GUUCAGGGAC AGUGCCUGGU GGGUAGUUUA ACUGGGGCGG UUGCCUCCUA AAAUGUAACG GAGGCGCCCA AAGGUUCCCU CAACCUGGAC GGCAAUCAGG UGUUGAGUGU AAGUGCACAA GGGAGCUUGA CUGCGAGACG GACAUGUCGA GCAGGGACGA AAGUCGGGAC UAGUGAUCCG GCACCUCUGA GUGGAAGGGG UGUCGCUCAA CGGAUAAAAG GUACCCCGGG GAUAACAGGC UGAUCUUCCC CAAGAGUCCA UAUCGACGGG AUGGUUUGGC ACCUCGAUGU CGGCUCGUCG CAUCCUGGGG CUGGAGCAGG UCCCAAGGGU UGGGCUGUUC GCCCAUUAAA GCGGCACGCG AGCUGGGUUU AGAACGUCGU GAGACAGUUC GGUCUCUAUC CGCCGCGCGC GUCAGAAGCU UGAGGAAACC UGUCCCUAGU ACGAGAGGAC CGGGACGGAC GAACCUCUGG UAUACCAGUU GUCCCACCAG GGGCACGGCU GGAUAGCCAC GUUCGGACAG GAUAACCGCU GAAAGCAUCU AAGCGGGAAA CCUCUUCCAA GACCAGGCUU CUCACCCUCU AGGAGGGAUA AGGCCCCCCG CAGACCACGG GAUUGAUAGA CCAGACCUGG AAGCCUAGUA AUAGGUGCAG GGAACUGGCA CUAACCGGCC GAAAACUUAC
MassTheoretical: 1.012140938 MDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #4: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUACGGCGG UCCAUAGCGG CAGGGAAACG CCCGGUCCCA UCCCGAACCC GGAAGCUAAG CCUGCCAGCG CCGAUGAUAC UACCCAUCCG GGUGGAAAAG UAGGACACCG CCGAACAC
MassTheoretical: 38.061816 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #5: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.425945 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #6: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.011393 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #7: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.920949 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #8: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.152328 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #9: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.483361 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #10: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Details: residues 44-73 modeled as poly-alanine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.949253 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #11: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.035736 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #12: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.023374 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #13: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.146689 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #14: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.400625 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #15: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.602244 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #16: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.77424 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #17: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.892246 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #18: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.711728 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #19: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.892806 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #20: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.494693 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #21: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.055894 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #22: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.3536 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #23: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.047836 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #24: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Details: residues 48-55 not modeled / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.228946 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #25: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.571078 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #26: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.249582 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #27: protein, LSU ribosomal protein L28P

ProteinName: LSU ribosomal protein L28P / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.891016 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #28: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.790895 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #29: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.022147 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #30: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.467719 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #31: protein, 50S ribosomal protein L33 1

ProteinName: 50S ribosomal protein L33 1Ribosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.468501 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #32: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.52258 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #33: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.298505 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #34: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.341277 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #35: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31
Details: residues 49-55 not modeled, intersubunit bridge forming protein
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.312485 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #36: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UUUUUGUUUG GAGAGUUUGA UCCUGGCUCA GGACGAACGC UGGCGGCGUG CUUAACACAU GCAAGUCGAA CGGAAAGGCC CUUUCGGGGG UACUCGAGUG GCGAACGGGU GAGUAACACG UGGGUGAUCU GCCCUGCACU UUGGGAUAAG CCUGGGAAAC UGGGUCUAAU ...Sequence:
UUUUUGUUUG GAGAGUUUGA UCCUGGCUCA GGACGAACGC UGGCGGCGUG CUUAACACAU GCAAGUCGAA CGGAAAGGCC CUUUCGGGGG UACUCGAGUG GCGAACGGGU GAGUAACACG UGGGUGAUCU GCCCUGCACU UUGGGAUAAG CCUGGGAAAC UGGGUCUAAU ACCGAAUACA CCCUGCUGGU CGCAUGGCCU GGUAGGGGAA AGCUUUUGCG GUGUGGGAUG GGCCCGCGGC CUAUCAGCUU GUUGGUGGGG UGAUGGCCUA CCAAGGCGAC GACGGGUAGC CGGCCUGAGA GGGUGACCGG CCACACUGGG ACUGAGAUAC GGCCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCGACGC CGCGUGAGGG AUGACGGCCU UCGGGUUGUA AACCUCUUUC AGCACAGACG AAGCGCAAGU GACGGUAUGU GCAGAAGAAG GACCGGCCAA CUACGUGCCA GCAGCCGCGG UAAUACGUAG GGUCCGAGCG UUGUCCGGAA UUACUGGGCG UAAAGAGCUC GUAGGUGGUU UGUCGCGUUG UUCGUGAAAA CUCACAGCUU AACUGUGGGC GUGCGGGCGA UACGGGCAGA CUAGAGUACU GCAGGGGAGA CUGGAAUUCC UGGUGUAGCG GUGGAAUGCG CAGAUAUCAG GAGGAACACC GGUGGCGAAG GCGGGUCUCU GGGCAGUAAC UGACGCUGAG GAGCGAAAGC GUGGGGAGCG AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGGU GGGUACUAGG UGUGGGUUUC CUUCCUUGGG AUCCGUGCCG UAGCUAACGC AUUAAGUACC CCGCCUGGGG AGUACGGCCG CAAGGCUAAA ACUCAAAGGA AUUGACGGGG GCCCGCACAA GCGGCGGAGC AUGUGGAUUA AUUCGAUGCA ACGCGAAGAA CCUUACCUGG GUUUGACAUG CACAGGACGC CGGCAGAGAU GUCGGUUCCC UUGUGGCCUG UGUGCAGGUG GUGCAUGGCU GUCGUCAGCU CGUGUCGUGA GAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUGUCU CAUGUUGCCA GCACGUUAUG GUGGGGACUC GUGAGAGACU GCCGGGGUCA ACUCGGAGGA AGGUGGGGAU GACGUCAAGU CAUCAUGCCC CUUAUGUCCA GGGCUUCACA CAUGCUACAA UGGCCGGUAC AAAGGGCUGC GAUGCCGUGA GGUGGAGCGA AUCCUUUCAA AGCCGGUCUC AGUUCGGAUC GGGGUCUGCA ACUCGACCCC GUGAAGUCGG AGUCGCUAGU AAUCGCAGAU CAGCAACGCU GCGGUGAAUA CGUUCCCGGG CCUUGUACAC ACCGCCCGUC ACGUCAUGAA AGUCGGUAAC ACCCGAAGCC GGUGGCCUAA CCCUUGUGGA GGGAGCCGUC GAAGGUGGGA UCGGCGAUUG GGACGAAGUC GUAACAAGGU AGCCGUACCG GAAGGUGCGG CUGGAUCACC UCCUUUCU
MassTheoretical: 495.373656 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #37: protein, Conserved domain protein

ProteinName: Conserved domain proteinProtein domain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.1643 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #38: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.191227 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #39: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.415787 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #40: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.94609 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #41: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.991637 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #42: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.660375 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #43: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.492638 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #44: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.794365 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #45: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.454313 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #46: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.671762 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #47: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.896366 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #48: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.249619 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #49: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type ZRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.976409 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #50: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.368097 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #51: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.795207 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #52: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.127002 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #53: protein, 30S ribosomal protein S18 2

ProteinName: 30S ribosomal protein S18 2Ribosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.524188 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #54: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.800602 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #55: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.556104 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #56: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.14523 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #57: nucleic-acid, P/P-site Phe-tRNA(Phe)

nucleic acidName: P/P-site Phe-tRNA(Phe) / Class: RNA
Details: Model and sequence adopted from Escherichia coli tRNA(Phe)
Structure: OTHER / Synthetic: No
Sequence:
GCCCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUGAAAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGG GCACCA
MassTheoretical: 24.485539 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #58: nucleic-acid, mRNA fragment

nucleic acidName: mRNA fragment / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUCU
MassTheoretical: 1.791053 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #59: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 625 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #60: ligand, ZINC ION

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

+
Component #61: ligand, PHENYLALANINE

LigandName: PHENYLALANINE
Details: Model and sequence adopted from Escherichia coli tRNA(Phe)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.165189 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: OTHER / Humidity: 96 %

-
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: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 100719.0 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionDetails: FEI EPU data collection

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 224584
3D reconstructionSoftware: RELION / CTF correction: CTF correction in Relion / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

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