5IMQ | pdb_00005imq

Structure of ribosome bound to cofactor at 3.8 angstrom resolution

Experimental Data Snapshot

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

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.8 of the entry. See complete history. 


Literature

Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome

Kumar, V., Ero, R., Ahmed, T., Goh, K.J., Zhan, Y., Bhushan, S., Gao, Y.G.

(2016) J Biological Chem 291: 12943-12950

  • DOI: https://doi.org/10.1074/jbc.M116.725945
  • Primary Citation of Related Structures:  
    5IMQ, 5IMR

  • PubMed Abstract: 

    Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, its exact biological function remains controversial. Here we present the cryo-EM reconstitution of the GTP form of EF4 bound to the ribosome with P and E site tRNAs at 3.8-Å resolution. Interestingly, our structure reveals an unrotated ribosome rather than a clockwise-rotated ribosome, as observed in the presence of EF4-GDP and P site tRNA. In addition, we also observed a counterclockwise-rotated form of the above complex at 5.7-Å resolution. Taken together, our results shed light on the interactions formed between EF4, the ribosome, and the P site tRNA and illuminate the GTPase activation mechanism at previously unresolved detail.

    • Organizational Affiliation: 
    • From the Institute of Molecular and Cell Biology, The Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, 138673 Singapore, the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36A [auth 1]37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10B [auth 2]173Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11C [auth 3]147Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2I [auth F]256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3J [auth G]239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4K [auth H]209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5L [auth I]162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6M [auth J]101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7N [auth K]156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8O [auth L]138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9P [auth M]128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10Q [auth N]105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11R [auth O]129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12S [auth P]132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13T [auth Q]126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZU [auth R]61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15V [auth S]89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16W [auth T]88Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17X [auth U]105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Y [auth V]88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19Z [auth W]93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AA [auth X]106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxBA [auth Y]27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1CA [auth Z]229Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2DA [auth a]276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3EA [auth b]206Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4FA [auth c]210Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5GA [auth d]182Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6HA [auth e]180Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13IA [auth f]140Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14JA [auth g]122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KA [auth h]150Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth i]141Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MA [auth j]118Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18NA [auth k]112Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OA [auth l]146Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PA [auth m]118Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QA [auth n]101Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RA [auth o]113Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SA [auth p]96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth q]110Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UA [auth r]206Thermus thermophilus HB8Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27VA [auth s]85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29WA [auth t]67Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30XA [auth u]60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31YA [auth v]71Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32ZA [auth w]60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AB [auth x]54Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BB [auth y]49Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CB [auth z]65Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 4DB [auth B]610Thermus thermophilus HB8Mutation(s): 0 
Gene Names: lepA, TTHA0741
EC: 3.6.5
UniProt
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Entity ID: 4
MoleculeChains LengthOrganismImage
P- site tRNAD [auth 4]77Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
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Entity ID: 5
MoleculeChains LengthOrganismImage
E site tRNAE [auth 5]76Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
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Entity ID: 6
MoleculeChains LengthOrganismImage
16S ribosomal RNAF [auth A]1,522Thermus thermophilus HB8
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Entity ID: 7
MoleculeChains LengthOrganismImage
23S ribosomal RNAG [auth D]2,893Thermus thermophilus HB8
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S ribosomal RNAH [auth E]123Thermus thermophilus HB8
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP
Download Ideal Coordinates CCD File 
EB [auth B]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Singapore National Research FoundationSingaporeNRF-RF2009- RF001-267

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Other
  • Version 1.2: 2016-06-01
    Changes: Other
  • Version 1.3: 2016-06-22
    Changes: Structure summary
  • Version 1.4: 2016-06-29
    Changes: Database references
  • Version 1.5: 2018-07-25
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Other
  • Version 1.6: 2019-12-18
    Changes: Advisory, Derived calculations, Source and taxonomy
  • Version 1.7: 2025-04-09
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.8: 2025-09-17
    Changes: Advisory, Derived calculations