4V7D

Structure of the Ribosome with Elongation Factor G Trapped in the Pre-Translocation State (pre-translocation 70S*tRNA*EF-G structure)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.5 of the entry. See complete history


Literature

Structure of the ribosome with elongation factor G trapped in the pretranslocation state.

Brilot, A.F.Korostelev, A.A.Ermolenko, D.N.Grigorieff, N.

(2013) Proc Natl Acad Sci U S A 110: 20994-20999

  • DOI: https://doi.org/10.1073/pnas.1311423110
  • Primary Citation of Related Structures:  
    4V7C, 4V7D

  • PubMed Abstract: 

    During protein synthesis, tRNAs and their associated mRNA codons move sequentially on the ribosome from the A (aminoacyl) site to the P (peptidyl) site to the E (exit) site in a process catalyzed by a universally conserved ribosome-dependent GTPase [elongation factor G (EF-G) in prokaryotes and elongation factor 2 (EF-2) in eukaryotes]. Although the high-resolution structure of EF-G bound to the posttranslocation ribosome has been determined, the pretranslocation conformation of the ribosome bound with EF-G and A-site tRNA has evaded visualization owing to the transient nature of this state. Here we use electron cryomicroscopy to determine the structure of the 70S ribosome with EF-G, which is trapped in the pretranslocation state using antibiotic viomycin. Comparison with the posttranslocation ribosome shows that the small subunit of the pretranslocation ribosome is rotated by ∼12° relative to the large subunit. Domain IV of EF-G is positioned in the cleft between the body and head of the small subunit outwardly of the A site and contacts the A-site tRNA. Our findings suggest a model in which domain IV of EF-G promotes the translocation of tRNA from the A to the P site as the small ribosome subunit spontaneously rotates back from the hybrid, rotated state into the nonrotated posttranslocation state.


  • Organizational Affiliation

    Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1C [auth AC]233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth AD]272Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth AE]209Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth AF]201Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth AG]178Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth AH]176Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth AI]149Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10J [auth AJ]165Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11K [auth AK]141Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L12L [auth AL]120Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13M [auth AM]142Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14N [auth AN]123Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15O [auth AO]144Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16P [auth AP]136Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17Q [auth AQ]127Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18R [auth AR]117Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19S [auth AS]114Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20T [auth AT]117Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21U [auth AU]103Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22V [auth AV]110Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23W [auth AW]100Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24X [auth AX]103Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25Y [auth AY]94Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Z [auth AZ]84Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28AA [auth A1]77Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29BA [auth A2]63Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30CA [auth A3]58Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DA [auth A4]56Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33EA [auth A5]54Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34FA [auth A6]46Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35GA [auth A7]64Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36HA [auth A8]38Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2JA [auth BB]240Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3KA [auth BC]232Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4LA [auth BD]205Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5MA [auth BE]166Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6NA [auth BF]131Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7OA [auth BG]178Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8PA [auth BH]129Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9QA [auth BI]129Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10RA [auth BJ]103Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11SA [auth BK]128Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12TA [auth BL]123Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13UA [auth BM]117Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14VA [auth BN]100Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15WA [auth BO]88Escherichia coliMutation(s): 0 
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UniProt GroupP0ADZ4
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16XA [auth BP]82Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17YA [auth BQ]83Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18ZA [auth BR]74Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AB [auth BS]91Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BB [auth BT]86Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21CB [auth BU]70Escherichia coliMutation(s): 0 
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Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation Factor GGB [auth BZ]711Escherichia coli K-12Mutation(s): 0 
Gene Names: fusA
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
viomycinHB [auth BY]6StreptomycesMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth AA]2,903Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth AB]119Escherichia coli
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Entity ID: 35
MoleculeChains LengthOrganismImage
16S ribosomal RNAIA [auth BA]1,542Escherichia coli
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Entity ID: 56
MoleculeChains LengthOrganismImage
tRNADB [auth BV],
EB [auth BW]
76Escherichia coli K-12
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Entity ID: 57
MoleculeChains LengthOrganismImage
mRNAFB [auth BX]18N/A
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
IB [auth A8]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
5OH
Query on 5OH
HB [auth BY]L-PEPTIDE LINKINGC6 H12 N4 O3ALA
DPP
Query on DPP
HB [auth BY]L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE
HB [auth BY]L-PEPTIDE LINKINGC6 H14 N2 O2LYS
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONIMAGIC
RECONSTRUCTIONRSAMPLE

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2014-12-17
    Changes: Source and taxonomy, Structure summary
  • Version 1.3: 2015-04-15
    Changes: Other
  • Version 1.4: 2018-07-18
    Changes: Data collection
  • Version 1.5: 2019-12-18
    Changes: Database references, Derived calculations, Other