5IMQ

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 

wwPDB Validation   3D Report Full Report


This is version 1.6 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 Biol Chem 291: 12943-12950

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

  • 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 ...

    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 the Institute of Structural Biology, Nanyang Technological University, 636921 Singapore ygao@ntu.edu.sg.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 137Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 2
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50S ribosomal protein L10 2173Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplJTTHA0209
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Entity ID: 3
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50S ribosomal protein L11 3147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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Entity ID: 9
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30S ribosomal protein S2 F256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 10
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30S ribosomal protein S3 G239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 11
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30S ribosomal protein S4 H209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 12
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30S ribosomal protein S5 I162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 13
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30S ribosomal protein S6 J101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 14
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30S ribosomal protein S7 K156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 15
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30S ribosomal protein S8 L138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 16
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30S ribosomal protein S9 M128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 17
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30S ribosomal protein S10 N105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 18
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30S ribosomal protein S11 O129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 P132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 20
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30S ribosomal protein S13 Q126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 21
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30S ribosomal protein S14 type Z R61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 22
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30S ribosomal protein S15 S89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 23
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30S ribosomal protein S16 T88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17 U105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
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30S ribosomal protein S18 V88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
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30S ribosomal protein S19 W93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 X106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein Thx Y27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 29
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50S ribosomal protein L1 Z229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L2 a276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 31
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50S ribosomal protein L3 b206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 32
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50S ribosomal protein L4 c210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 d182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 e180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13 f140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14 g122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 h150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 38
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50S ribosomal protein L16 i141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 j118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 40
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50S ribosomal protein L18 k112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 41
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50S ribosomal protein L19 l146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20 m118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 43
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50S ribosomal protein L21 n101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 o113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 45
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50S ribosomal protein L23 p96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 46
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50S ribosomal protein L24 q110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 47
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50S ribosomal protein L25 r206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 48
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50S ribosomal protein L27 s85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 49
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50S ribosomal protein L29 t67Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
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50S ribosomal protein L30 u60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 51
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50S ribosomal protein L31 v71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 52
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50S ribosomal protein L32 w60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 53
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50S ribosomal protein L33 x54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 54
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50S ribosomal protein L34 y49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 55
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50S ribosomal protein L35 z65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 4 B610Thermus thermophilus HB8Mutation(s): 0 
Gene Names: lepATTHA0741
EC: 3.6.5
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Entity ID: 4
MoleculeChainsLengthOrganismImage
P- site tRNA477Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
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Entity ID: 5
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E site tRNA576Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
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Entity ID: 6
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16S ribosomal RNAA1522Thermus thermophilus HB8
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Entity ID: 7
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23S ribosomal RNAD2893Thermus thermophilus HB8
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Entity ID: 8
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5S ribosomal RNAE123Thermus thermophilus HB8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
B
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-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
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