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- EMDB-3748: Cryo-EM reconstruction of the small subunit of the Mycobacterium ... -

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Entry
Database: EMDB / ID: EMD-3748
TitleCryo-EM reconstruction of the small subunit of the Mycobacterium smegmatis ribosome
Map data
Sample30S small ribosomal subunit:
(nucleic-acidNucleic acid) x 3 / Conserved domain proteinProtein domain / (30S ribosomal protein ...) x 19 / 50S ribosomal protein L31 / (ligand) x 2
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / metal ion binding
Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S7 domain superfamily / Ribosomal protein S13, conserved site / Ribosomal protein S5, N-terminal, conserved site ...Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S7 domain superfamily / Ribosomal protein S13, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, N-terminal / Domain of unknown function DUF1713 / 30S ribosomal protein S17 / Ribosomal protein S9, conserved site / Ribosomal protein S13-like, H2TH / Ribosomal protein S7 domain / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / L28p-like / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S19/S15, superfamily / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Nucleic acid-binding, OB-fold / S15/NS1, RNA-binding / Ribosomal protein S20 superfamily / Ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S14 / Ribosomal protein S5 / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S16 / K homology domain superfamily, prokaryotic type / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L31 superfamily / Ribosomal protein S14/S29 / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S12, bacterial-type / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S3, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15, bacterial-type / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein L31 / Ribosomal protein S11 / Ribosomal protein S3, C-terminal domain superfamily
30S ribosomal protein S13 / 50S ribosomal protein L31 / 30S ribosomal protein S20 / 30S ribosomal protein S15 / 30S ribosomal protein S2 / 30S ribosomal protein S16 / 30S ribosomal protein S9 / 30S ribosomal protein S4 / 30S ribosomal protein S11 / 30S ribosomal protein S17 ...30S ribosomal protein S13 / 50S ribosomal protein L31 / 30S ribosomal protein S20 / 30S ribosomal protein S15 / 30S ribosomal protein S2 / 30S ribosomal protein S16 / 30S ribosomal protein S9 / 30S ribosomal protein S4 / 30S ribosomal protein S11 / 30S ribosomal protein S17 / 30S ribosomal protein S5 / 30S ribosomal protein S8 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S3 / 30S ribosomal protein S19 / 30S ribosomal protein S10 / 30S ribosomal protein S7 / 30S ribosomal protein S12 / Conserved domain protein / 30S ribosomal protein S6 / 30S ribosomal protein S18 2
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5o5j
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5o5j
  • 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_3748.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-0.23724163 - 0.55080956
Average (Standard dev.)0.0017705566 (±0.030618884)
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-0.2370.5510.002

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Supplemental data

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Sample components

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Entire 30S small ribosomal subunit

EntireName: 30S small ribosomal subunit / Number of components: 27

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Component #1: protein, 30S small ribosomal subunit

ProteinName: 30S small ribosomal subunit / Recombinant expression: No
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #2: 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)

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Component #3: 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)

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Component #4: 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)

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Component #5: 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)

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Component #6: 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)

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Component #7: 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)

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Component #8: 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)

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Component #9: 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)

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Component #10: 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)

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Component #11: 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)

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Component #12: 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)

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Component #13: 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)

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Component #14: 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)

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Component #15: 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)

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Component #16: 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)

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Component #17: 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)

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Component #18: 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)

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Component #19: 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)

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Component #20: 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)

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Component #21: 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)

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Component #22: 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)

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Component #23: nucleic-acid, tRNA-Phe anticodon stem

nucleic acidName: tRNA-Phe anticodon stem / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGGGGAUUGA AAAUCCCCG
MassTheoretical: 6.140736 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #24: 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)

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Component #25: 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)

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Component #26: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 217 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #27: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

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

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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)

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Image acquisition

Image acquisitionDetails: FEI EPU data collection

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 224584
3D reconstructionSoftware: RELION / CTF correction: CTF correction in Relion / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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