RCSB PDB - 5OT7: Elongation factor G-ribosome complex captures in the absence of inhibitors.

 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25F [auth 6]178Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9G [auth 7]146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2H [auth A]235Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3I [auth B]207Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4J [auth C]208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5K [auth D]151Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6L [auth E]101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7M [auth F]155Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8N [auth G]138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9O [auth H]127Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10P [auth I]99Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11Q [auth J]119Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12R [auth K]125Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13S [auth L]119Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZT [auth M]60Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15U [auth N]88Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16V [auth O]84Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17W [auth P]100Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18X [auth Q]70Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19Y [auth R]88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20Z [auth S]99Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxAA [auth T]25Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor GBA [auth U]687Thermus thermophilus HB8Mutation(s): 0 
Gene Names: fusAfusTTHA1695
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27CA [auth V]78Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28DA [auth W]94Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29EA [auth X]71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30FA [auth Y]60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31GA [auth Z]71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32HA [auth a]59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33IA [auth b]50Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34JA [auth c]48Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35KA [auth d]64Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36LA [auth e]37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1MA [auth f]227Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2NA [auth g]275Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3OA [auth h]205Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4PA [auth i]208Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5QA [auth j]179Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6RA [auth k]176Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL10SA [auth l]130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL11TA [auth m]140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein bL12UA [auth n]71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13VA [auth o]139Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14WA [auth p]122Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15XA [auth q]150Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16YA [auth r]141Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17ZA [auth s]118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18AB [auth t]99Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19BB [auth u]138Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20CB [auth v]117Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21DB [auth w]101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22EB [auth x]113Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23FB [auth y]93Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24GB [auth z]101Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
US [auth U]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN

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NS [auth C],
PS [auth M],
XS [auth e]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 1]
AD [auth 1]
AE [auth 1]
AF [auth 1]
AG [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.12rc1-2807

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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