2P8Z

Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDPNP:sordarin cryo-EM reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of modified eEF2.80S ribosome complexes reveal the role of GTP hydrolysis in translocation.

Taylor, D.J.Nilsson, J.Merrill, A.R.Andersen, G.R.Nissen, P.Frank, J.

(2007) EMBO J 26: 2421-2431

  • DOI: https://doi.org/10.1038/sj.emboj.7601677
  • Primary Citation of Related Structures:  
    2P8W, 2P8X, 2P8Y, 2P8Z

  • PubMed Abstract: 

    On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 in eukaryotes, EF-G in bacteria). We have obtained cryo-EM reconstructions of eukaryotic ribosomes complexed with ADP-ribosylated eEF2 (ADPR-eEF2), before and after GTP hydrolysis, providing a structural basis for analyzing the GTPase-coupled mechanism of translocation. Using the ADP-ribosyl group as a distinct marker, we observe conformational changes of ADPR-eEF2 that are due strictly to GTP hydrolysis. These movements are likely representative of native eEF2 motions in a physiological context and are sufficient to uncouple the mRNA-tRNA complex from two universally conserved bases in the ribosomal decoding center (A1492 and A1493 in Escherichia coli) during translocation. Interpretation of these data provides a detailed two-step model of translocation that begins with the eEF2/EF-G binding-induced ratcheting motion of the small ribosomal subunit. GTP hydrolysis then uncouples the mRNA-tRNA complex from the decoding center so translocation of the mRNA-tRNA moiety may be completed by a head rotation of the small subunit.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Health Research Inc.,Wadsworth Center, Albany, NY 12201-0509, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2A [auth T]842Saccharomyces cerevisiaeMutation(s): 1 
UniProt
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32324 
Go to UniProtKB:  P32324
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32324
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu-BB [auth S]35Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P60339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60339 
Go to UniProtKB:  P60339
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60339
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download Ideal Coordinates CCD File 
C [auth T]ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
GNP
Query on GNP

Download Ideal Coordinates CCD File 
E [auth T]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
SO1
Query on SO1

Download Ideal Coordinates CCD File 
D [auth T][1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID
C27 H42 O8
DIBGPTPYRVEPSP-OHFCZZTFSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DDE
Query on DDE
A [auth T]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Database references, Derived calculations, Other