5J8B

Crystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Elongation factor 4 remodels the A-site tRNA on the ribosome.

Gagnon, M.G.Lin, J.Steitz, T.A.

(2016) Proc Natl Acad Sci U S A 113: 4994-4999

  • DOI: 10.1073/pnas.1522932113
  • Primary Citation of Related Structures:  
    5J8B

  • PubMed Abstract: 
  • During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote ...

    During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. The structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114; Department of Chemistry, Yale University, New Haven, CT 06520-8107 thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1C228Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P27150 (Thermus thermophilus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2D276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3E206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4F210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5G182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6H180Thermus thermophilus HB8Mutation(s): 0 
Find proteins for A0A0M9ADP1 (Thermus aquaticus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10J173Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplJTTHA0209
Find proteins for Q8VVE3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11K147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
Find proteins for Q5SLP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13N140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14O122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15P150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16Q141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17R118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18S112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19T146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20U118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 19
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50S ribosomal protein L21V101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22W113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23X96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24Y110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25Z206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 26
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50S ribosomal protein L29272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 27
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50S ribosomal protein L30360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2b256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3c239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4d209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5e162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6f101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 40
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30S ribosomal protein S7g156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8h138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9i128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 43
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30S ribosomal protein S10j105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 44
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30S ribosomal protein S11k129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 45
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30S ribosomal protein S12l132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 46
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30S ribosomal protein S13m126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Zn61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 48
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30S ribosomal protein S15o89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16p88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 50
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30S ribosomal protein S17q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18r88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 52
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30S ribosomal protein S19s93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 53
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30S ribosomal protein S20t106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 54
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30S ribosomal protein Thxu27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
GDPCP fused to the N-terminus of the ribosomal protein L9,Elongation factor 4z679Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
EC: 3.6.5
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNAA2915Thermus thermophilus HB8
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Entity ID: 2
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5S Ribosomal RNAB121Thermus thermophilus HB8
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Entity ID: 34
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAa1521Thermus thermophilus HB8
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Entity ID: 55
MoleculeChainsLengthOrganismImage
mRNAv24Thermus thermophilus HB8
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Entity ID: 56
MoleculeChainsLengthOrganismImage
A-site tRNAw76Thermus thermophilus HB8
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Entity ID: 57
MoleculeChainsLengthOrganismImage
P-site tRNAx77Thermus thermophilus HB8
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Entity ID: 58
MoleculeChainsLengthOrganismImage
E-site tRNAy76Thermus thermophilus HB8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

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z
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

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d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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4, 5, 6, 9, Y, n
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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0, 5, 6, 7, 8, 9, A, B, D, E, F, G, H, N, O, P, Q, R, U, V, W, X, Z, a, d, e, f, l, m, n, v, x, z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.124α = 90
b = 271.723β = 90
c = 436.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM022778

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations
  • Version 2.0: 2019-07-03
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2019-12-25
    Changes: Author supporting evidence