[English] 日本語
Yorodumi
- EMDB-3750: Cryo-EM reconstruction of the large subunit of the Mycobacterium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3750
TitleCryo-EM reconstruction of the large subunit of the Mycobacterium smegmatis ribosome
Map data
Sample50S large ribosomal subunit:
(50S ribosomal protein ...) x 32 / (nucleic-acidNucleic acid) x 3 / (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 / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome ...large ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / ribosome biogenesis / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / metal ion binding
Ribosomal protein L25, beta domain / Ribosomal protein L3, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal domain superfamily ...Ribosomal protein L25, beta domain / Ribosomal protein L3, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L2, domain 3 / Ribosomal protein L2, domain 2 / Ribosomal protein L5, bacterial-type / Ribosomal protein L18e/L15P / 50S ribosomal protein uL4 / Ribosomal protein L20, C-terminal / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein L36 superfamily / L28p-like / Ribosomal protein L35 / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein L28/L24 / Ribosomal protein L4 domain superfamily / Ribosomal protein L10 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L25/L23 / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L36 / Ribosomal protein L21 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L33 / Ribosomal protein L27 / Ribosomal protein L28 / Ribosomal protein L15, conserved site / Ribosomal protein L22/L17 / Ribosomal protein L25, long-form / Ribosomal protein L23/L25, conserved site / Ribosomal protein L11/L12 / Ribosomal protein L6 / Ribosomal protein L3 / Ribosomal protein L17 / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L34 / Ribosomal protein L9 / Ribosomal protein L14P / Ribosomal protein L16 / Ribosomal protein L25, C-terminal / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L31 superfamily / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L29/L35 / Ribosomal protein L19 / Ribosomal protein L5 / Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9/RNase H1, N-terminal / Translation protein, beta-barrel domain superfamily / Translation protein SH3-like domain superfamily / Ribosomal protein L11, bacterial-type
50S ribosomal protein L20 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / Uncharacterized protein / 50S ribosomal protein L28 / 50S ribosomal protein L19 / 50S ribosomal protein L31 / 50S ribosomal protein L35 / 50S ribosomal protein L27 / 50S ribosomal protein L21 ...50S ribosomal protein L20 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / Uncharacterized protein / 50S ribosomal protein L28 / 50S ribosomal protein L19 / 50S ribosomal protein L31 / 50S ribosomal protein L35 / 50S ribosomal protein L27 / 50S ribosomal protein L21 / 50S ribosomal protein L15 / 50S ribosomal protein L25 / 50S ribosomal protein L32 / 50S ribosomal protein L9 / 50S ribosomal protein L36 / 50S ribosomal protein L24 / 50S ribosomal protein L30 / 50S ribosomal protein L18 / 50S ribosomal protein L6 / 50S ribosomal protein L5 / 50S ribosomal protein L14 / 50S ribosomal protein L29 / 50S ribosomal protein L16 / 50S ribosomal protein L22 / 50S ribosomal protein L2 / 50S ribosomal protein L23 / 50S ribosomal protein L4 / 50S ribosomal protein L3 / 50S ribosomal protein L10 / 50S ribosomal protein L11 / 50S ribosomal protein L33 1 / 50S ribosomal protein L34
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsHentschel J / Burnside C / Mignot I / Leibundgut M / Boehringer D / Ban N
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_163478 Switzerland
NCCR RNA and disease program, SNSF51NF40_141735 Switzerland
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 2, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseJul 12, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5o60
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5o60
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_3750.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: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.25450435 - 0.56970584
Average (Standard dev.)0.0019694762 (±0.036407027)
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-0.2550.5700.002

-
Supplemental data

-
Sample components

+
Entire 50S large ribosomal subunit

EntireName: 50S large ribosomal subunit / Number of components: 39

+
Component #1: protein, 50S large ribosomal subunit

ProteinName: 50S large ribosomal subunit / Recombinant expression: No
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
Component #10: protein, 50S ribosomal protein L9

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

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
Component #24: protein, 50S ribosomal protein L24

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

+
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)

+
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)

+
Component #27: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.891016 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
Component #35: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.312485 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #36: nucleic-acid, tRNA CCA-end acetylated (Phe)

nucleic acidName: tRNA CCA-end acetylated (Phe) / Class: RNA / Details: tRNA CCA polyribonucleotid, acetylated (Phe) / Structure: OTHER / Synthetic: No
Sequence:
CCA
MassTheoretical: 0.894612 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Component #37: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 408 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #38: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #39: ligand, PHENYLALANINE

LigandName: PHENYLALANINE / Details: tRNA CCA polyribonucleotid, acetylated (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: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more