5IMR | pdb_00005imr

Structure of ribosome bound to cofactor at 5.7 angstrom resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 2,310.42 kDa 
  • Atom Count: 152,879 
  • Modeled Residue Count: 11,299 
  • Deposited Residue Count: 11,663 
  • Unique protein chains: 51
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth F]256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth G]239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth H]209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth I]162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth J]101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth K]156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth L]138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth M]128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth N]105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth O]129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth P]132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth Q]126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth R]61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth S]89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth T]88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth U]105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth V]88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth W]93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth X]106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth Y]27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor 4V [auth C]610Thermus thermophilus HB8Mutation(s): 0 
Gene Names: lepA, TTHA0741
EC: 3.6.5
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L1Y [auth Z]229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Z [auth a]276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3AA [auth b]206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4BA [auth c]210Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5CA [auth d]182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6DA [auth e]180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13EA [auth f]140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14FA [auth g]122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15GA [auth h]150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16HA [auth i]141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17IA [auth j]118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18JA [auth k]112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19KA [auth l]146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20LA [auth m]118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21MA [auth n]101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22NA [auth o]113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23OA [auth p]96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PA [auth q]110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L25QA [auth r]206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27RA [auth s]85Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29SA [auth t]67Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30TA [auth u]60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31UA [auth v]71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth w]60Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33WA [auth x]54Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34XA [auth y]49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35YA [auth z]65Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36ZA [auth 1]37Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L10AB [auth 2]173Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q8VVE3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L11BB [auth 3]147Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SLP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,522Thermus thermophilus HB8
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S ribosomal RNAW [auth D]2,893Thermus thermophilus HB8
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Entity ID: 24
MoleculeChains LengthOrganismImage
5S ribosomal RNAX [auth E]123Thermus thermophilus HB8
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Entity ID: 55
MoleculeChains LengthOrganismImage
P site- tRNACB [auth 4]77Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
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Entity ID: 56
MoleculeChains LengthOrganismImage
E site- tRNADB [auth 5]76Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP

Query on GCP


Download:Ideal Coordinates CCD File
EB [auth C]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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: 2017-09-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.6: 2018-07-25
    Changes: Data collection, Other
  • Version 1.7: 2019-12-18
    Changes: Advisory, Derived calculations, Source and taxonomy
  • Version 1.8: 2024-10-09
    Changes: Data collection, Database references, Refinement description, Structure summary