1ZM9 | pdb_00001zm9

Structure of eEF2-ETA in complex with PJ34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.274 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.254 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history

Literature

Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry.

Joergensen, R.Merrill, A.R.Yates, S.P.Marquez, V.E.Schwan, A.L.Boesen, T.Andersen, G.R.

(2005) Nature 436: 979-984

  • DOI: https://doi.org/10.1038/nature03871
  • Primary Citation Related Structures: 
    1ZM2, 1ZM3, 1ZM4, 1ZM9

  • PubMed Abstract: 

    The bacteria causing diphtheria, whooping cough, cholera and other diseases secrete mono-ADP-ribosylating toxins that modify intracellular proteins. Here, we describe four structures of a catalytically active complex between a fragment of Pseudomonas aeruginosa exotoxin A (ETA) and its protein substrate, translation elongation factor 2 (eEF2). The target residue in eEF2, diphthamide (a modified histidine), spans across a cleft and faces the two phosphates and a ribose of the non-hydrolysable NAD+ analogue, betaTAD. This suggests that the diphthamide is involved in triggering NAD+ cleavage and interacting with the proposed oxacarbenium intermediate during the nucleophilic substitution reaction, explaining the requirement of diphthamide for ADP ribosylation. Diphtheria toxin may recognize eEF2 in a manner similar to ETA. Notably, the toxin-bound betaTAD phosphates mimic the phosphate backbone of two nucleotides in a conformational switch of 18S rRNA, thereby achieving universal recognition of eEF2 by ETA.


  • Organizational Affiliation
    • Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000, Denmark.

Macromolecule Content 

  • Total Structure Weight: 349.02 kDa 
  • Atom Count: 24,042 
  • Modeled Residue Count: 3,090 
  • Deposited Residue Count: 3,147 
  • Unique protein chains: 2

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor 2
A, C, E
842Saccharomyces cerevisiaeMutation(s): 1 
EC: 3.6.5
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
exotoxin A
B, D, F
207Pseudomonas aeruginosaMutation(s): 0 
EC: 2.4.2.36
UniProt
Find proteins for P11439 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P11439 
Go to UniProtKB:  P11439
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11439
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DDE
Query on DDE
A, C, E
L-PEPTIDE LINKINGC13 H24 N5 O3HIS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.274 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.254 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 330.84α = 90
b = 68.74β = 103.5
c = 191.46γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
MOLREPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description