2A19

PKR kinase domain- eIF2alpha- AMP-PNP complex.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Higher-Order Substrate Recognition of eIF2alpha by the RNA-Dependent Protein Kinase PKR.

Dar, A.C., Dever, T.E., Sicheri, F.

(2005) Cell 122: 887-900

  • DOI: 10.1016/j.cell.2005.06.044
  • Primary Citation of Related Structures:  
    2A19, 2A1A

  • PubMed Abstract: 

    • In response to binding viral double-stranded RNA byproducts within a cell, the RNA-dependent protein kinase PKR phosphorylates the alpha subunit of the translation initiation factor eIF2 on a regulatory site, Ser51. This triggers the general shutdown ...

    In response to binding viral double-stranded RNA byproducts within a cell, the RNA-dependent protein kinase PKR phosphorylates the alpha subunit of the translation initiation factor eIF2 on a regulatory site, Ser51. This triggers the general shutdown of protein synthesis and inhibition of viral propagation. To understand the basis for substrate recognition by and the regulation of PKR, we determined X-ray crystal structures of the catalytic domain of PKR in complex with eIF2alpha. The structures reveal that eIF2alpha binds to the C-terminal catalytic lobe while catalytic-domain dimerization is mediated by the N-terminal lobe. In addition to inducing a local unfolding of the Ser51 acceptor site in eIF2alpha, its mode of binding to PKR affords the Ser51 site full access to the catalytic cleft of PKR. The generality and implications of the structural mechanisms uncovered for PKR to the larger family of four human eIF2alpha protein kinases are discussed.

    Organizational Affiliation: 

    Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 alpha subunitA175Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUI2, TIF211
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20459 
Go to UniProtKB:  P20459
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-induced, double-stranded RNA-activated protein kinaseB, C284Homo sapiensMutation(s): 3 
Gene Names: PRKR, EIF2AK2, PKR
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt), 2.7.10.2 (UniProt)
Find proteins for P19525 (Homo sapiens)
Explore P19525 
Go to UniProtKB:  P19525
NIH Common Fund Data Resources
PHAROS  P19525
GTEx  ENSG00000055332
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		B,CL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.659α = 90
b = 48.75β = 98.44
c = 133.434γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance