5OT7

Elongation factor G-ribosome complex captures in the absence of inhibitors.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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 structure of an elongation factor G-ribosome complex captured in the absence of inhibitors.

Mace, K.Giudice, E.Chat, S.Gillet, R.

(2018) Nucleic Acids Res 46: 3211-3217

  • DOI: 10.1093/nar/gky081
  • Primary Citation of Related Structures:  
    5OT7

  • PubMed Abstract: 
  • During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome complexes have been obtained by trapping EF-G in the ribosome. ...

    During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome complexes have been obtained by trapping EF-G in the ribosome. These results were based on use of non-hydrolyzable guanosine 5'-triphosphate (GTP) analogs, specific inhibitors or a mutated EF-G form. Here, we present the first cryo-electron microscopy structure of EF-G bound to ribosome in the absence of an inhibitor. The structure reveals a natural conformation of EF-G·GDP in the ribosome, with a previously unseen conformation of its third domain. These data show how EF-G must affect translocation, and suggest the molecular mechanism by which fusidic acid antibiotic prevents the release of EF-G after GTP hydrolysis.


    Organizational Affiliation

    Univ. Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, F35000 Rennes, France.



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 6178Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 7
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50S ribosomal protein L9 7146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 A235Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 B207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 C208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 D151Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 12
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30S ribosomal protein S6 E101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 13
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30S ribosomal protein S7 F155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 G138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 15
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30S ribosomal protein S9 H127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 I99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 17
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30S ribosomal protein S11 J119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 K125Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13 L119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z M60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15 N88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16 O84Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17 P100Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18 Q70Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 S99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein Thx T25Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor G U687Thermus thermophilus HB8Mutation(s): 0 
Gene Names: fusAfusTTHA1695
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Entity ID: 29
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50S ribosomal protein L27 V78Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 30
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50S ribosomal protein L28 W94Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 X71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 Y60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 33
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50S ribosomal protein L31 Z71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 a59Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 b50Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 c48Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 d64Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 38
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50S ribosomal protein L36 e37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 39
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50S ribosomal protein L1 f227Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 40
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50S ribosomal protein L2 g275Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3 h205Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 i208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 j179Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 k176Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uL10 l130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
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Ribosomal protein uL11 m140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
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Ribosomal protein bL12 n71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
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50S ribosomal protein L13 o139Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14 p122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 q150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 r141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 52
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50S ribosomal protein L17 s118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 53
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50S ribosomal protein L18 t99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 54
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50S ribosomal protein L19 u138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 55
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50S ribosomal protein L20 v117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 56
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50S ribosomal protein L21 w101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 x113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 58
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50S ribosomal protein L23 y93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 59
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50S ribosomal protein L24 z101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S Ribosomal RNA11507Thermus thermophilus HB8
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Entity ID: 2
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tRNA-Phe276Escherichia coli
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    mRNA315Escherichia coli
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    Entity ID: 4
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    23S Ribosomal RNA42901Thermus thermophilus HB8
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    Entity ID: 5
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    5S Ribosomal RNA5119Thermus thermophilus HB8
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GDP
    Query on GDP

    Download Ideal Coordinates CCD File 
    U
    GUANOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O11 P2
    QGWNDRXFNXRZMB-UUOKFMHZSA-N
     Ligand Interaction
    ZN
    Query on ZN

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

    Download Ideal Coordinates CCD File 
    1, 4, D, O, S, U, c, e, h, i, q, t, u, x
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.80 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    French National Research AgencyFranceANR-14-ASTR-0001
    GENCIFrancei2015037391

    Revision History 

    • Version 1.0: 2018-02-14
      Type: Initial release
    • Version 1.1: 2018-02-21
      Changes: Structure summary
    • Version 1.2: 2018-02-28
      Changes: Author supporting evidence
    • Version 1.3: 2018-04-11
      Changes: Data collection, Database references