5IMR

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 

wwPDB Validation   3D Report Full Report


This is version 1.7 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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth F]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
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30S ribosomal protein S3C [auth G]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth H]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth I]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth J]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
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30S ribosomal protein S7G [auth K]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth L]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 9
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30S ribosomal protein S9I [auth M]128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
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30S ribosomal protein S10J [auth N]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
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30S ribosomal protein S11K [auth O]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
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30S ribosomal protein S12L [auth P]132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
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30S ribosomal protein S13M [auth Q]126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
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30S ribosomal protein S14 type ZN [auth R]61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth S]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
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30S ribosomal protein S16P [auth T]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
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30S ribosomal protein S17Q [auth U]105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
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30S ribosomal protein S18R [auth V]88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth W]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth X]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
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30S ribosomal protein ThxU [auth Y]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 4V [auth C]610Thermus thermophilus HB8Mutation(s): 0 
Gene Names: lepATTHA0741
EC: 3.6.5
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Entity ID: 25
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50S ribosomal protein L1Y [auth Z]229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L2Z [auth a]276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 27
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50S ribosomal protein L3AA [auth b]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4BA [auth c]210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 29
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50S ribosomal protein L5CA [auth d]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 30
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50S ribosomal protein L6DA [auth e]180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13EA [auth f]140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14FA [auth g]122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L15GA [auth h]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 34
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50S ribosomal protein L16HA [auth i]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 35
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50S ribosomal protein L17IA [auth j]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 36
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50S ribosomal protein L18JA [auth k]112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 37
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50S ribosomal protein L19KA [auth l]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 38
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50S ribosomal protein L20LA [auth m]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 39
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50S ribosomal protein L21MA [auth n]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 40
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50S ribosomal protein L22NA [auth o]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 41
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50S ribosomal protein L23OA [auth p]96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 42
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50S ribosomal protein L24PA [auth q]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 43
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50S ribosomal protein L25QA [auth r]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 44
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50S ribosomal protein L27RA [auth s]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 45
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50S ribosomal protein L29SA [auth t]67Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
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50S ribosomal protein L30TA [auth u]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 47
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50S ribosomal protein L31UA [auth v]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 48
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50S ribosomal protein L32VA [auth w]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 49
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50S ribosomal protein L33WA [auth x]54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 50
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50S ribosomal protein L34XA [auth y]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 51
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50S ribosomal protein L35YA [auth z]65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 52
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50S ribosomal protein L36ZA [auth 1]37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 53
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50S ribosomal protein L10AB [auth 2]173Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplJTTHA0209
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Entity ID: 54
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50S ribosomal protein L11BB [auth 3]147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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Entity ID: 1
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16S ribosomal RNAA1522Thermus thermophilus HB8
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Entity ID: 23
MoleculeChainsLengthOrganismImage
23S ribosomal RNAW [auth D]2893Thermus thermophilus HB8
Protein Feature View
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Entity ID: 24
MoleculeChainsLengthOrganismImage
5S ribosomal RNAX [auth E]123Thermus thermophilus HB8
Protein Feature View
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Entity ID: 55
MoleculeChainsLengthOrganismImage
P site- tRNACB [auth 4]77Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
Protein Feature View
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Entity ID: 56
MoleculeChainsLengthOrganismImage
E site- tRNADB [auth 5]76Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 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: 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