5O5J

Structure of the 30S small ribosomal subunit from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.

Hentschel, J.Burnside, C.Mignot, I.Leibundgut, M.Boehringer, D.Ban, N.

(2017) Cell Rep 20: 149-160

  • DOI: 10.1016/j.celrep.2017.06.029
  • Primary Citation of Related Structures:  
    5O61, 5O60, 5O5J

  • PubMed 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 worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance ...

    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.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Conserved domain protein B33Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0945
Find proteins for A0QR10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 C275Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsCMSMEG_1442MSMEI_1406
Find proteins for A0QSD7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 D201Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsDMSMEG_1523MSMEI_1487
Find proteins for A0QSL7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 E214Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsEMSMEG_1472MSMEI_1436
Find proteins for A0QSG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 F96Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Find proteins for A0A0D6J3X3 (Mycolicibacterium smegmatis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7 G156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsGMSMEG_1399MSMEI_1361
Find proteins for A0QS97 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 H132Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsHMSMEG_1469MSMEI_1433
Find proteins for A0QSG3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9 I150Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsIMSMEG_1557MSMEI_1520
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 10
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30S ribosomal protein S10 J101Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsJMSMEG_1435MSMEI_1399
Find proteins for A0QSD0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11 K138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsKMSMEG_1522MSMEI_1486
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
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30S ribosomal protein S12 L124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsLMSMEG_1398MSMEI_1360
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13 M124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsMMSMEG_1521MSMEI_1485
Find proteins for A0QSL5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z N61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsZrpsNMSMEG_1468MSMEI_1432
Find proteins for A0QSG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15 O89Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsOMSMEG_2654MSMEI_2591
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16 P156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsPMSMEG_2435MSMEI_2374
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17 Q98Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsQMSMEG_1445MSMEI_1409
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18 2 R84Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsR2rpsR1MSMEG_6895MSMEI_6711
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 S93Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsSMSMEG_1440MSMEI_1404
Find proteins for A0QSD5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 T86Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsTMSMEG_4571MSMEI_4459
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 V277Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsBMSMEG_2519MSMEI_2460
Find proteins for A0QVB8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 g75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmEMSMEG_4951MSMEI_4823
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1528Mycolicibacterium smegmatis MC2 155
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  • Entity ID: 22
    MoleculeChainsLengthOrganismImage
    tRNA-Phe anticodon stemW19Mycolicibacterium smegmatis MC2 155
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    • Entity ID: 23
      MoleculeChainsLengthOrganismImage
      mRNA fragmentX6Mycolicibacterium smegmatis MC2 155
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      N, R
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      A, F, R
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 3.45 Å
      • Aggregation State: PARTICLE 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Swiss National Science FoundationSwitzerland310030B_163478
      NCCR RNA and disease program, SNSFSwitzerland51NF40_141735

      Revision History  (Full details and data files)

      • Version 1.0: 2017-07-12
        Type: Initial release
      • Version 1.1: 2017-07-19
        Changes: Database references
      • Version 1.2: 2018-10-17
        Changes: Data collection, Refinement description
      • Version 1.3: 2019-12-11
        Changes: Other