2BE1

Structure of the compact lumenal domain of yeast Ire1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inaugural Article: On the mechanism of sensing unfolded protein in the endoplasmic reticulum

Credle, J.J.Finer-Moore, J.S.Papa, F.R.Stroud, R.M.Walter, P.

(2005) Proc Natl Acad Sci U S A 102: 18773-18784

  • DOI: 10.1073/pnas.0509487102
  • Primary Citation of Related Structures:  
    2BE1

  • PubMed Abstract: 
  • Unfolded proteins in the endoplasmic reticulum (ER) activate the ER transmembrane sensor Ire1 to trigger the unfolded protein response (UPR), a homeostatic signaling pathway that adjusts ER protein folding capacity according to need. Ire1 is a bifunc ...

    Unfolded proteins in the endoplasmic reticulum (ER) activate the ER transmembrane sensor Ire1 to trigger the unfolded protein response (UPR), a homeostatic signaling pathway that adjusts ER protein folding capacity according to need. Ire1 is a bifunctional enzyme, containing cytoplasmic kinase and RNase domains whose roles in signal transduction downstream of Ire1 are understood in some detail. By contrast, the question of how its ER-luminal domain (LD) senses unfolded proteins has remained an enigma. The 3.0-A crystal structure and consequent structure-guided functional analyses of the conserved core region of the LD (cLD) leads us to a proposal for the mechanism of response. cLD exhibits a unique protein fold and is sufficient to control Ire1 activation by unfolded proteins. Dimerization of cLD monomers across a large interface creates a shared central groove formed by alpha-helices that are situated on a beta-sheet floor. This groove is reminiscent of the peptide binding domains of major histocompatibility complexes (MHCs) in its gross architecture. Conserved amino acid side chains in Ire1 that face into the groove are shown to be important for UPR activation in that their mutation reduces the response. Mutational analyses suggest that further interaction between cLD dimers is required to form higher-order oligomers necessary for UPR activation. We propose that cLD directly binds unfolded proteins, which changes the quaternary association of the monomers in the membrane plane. The changes in the ER lumen in turn position Ire1 kinase domains in the cytoplasm optimally for autophosphorylation to initiate the UPR.


    Organizational Affiliation

    Howard Hughes Medical Institute, Departments of Biochemistry and Biophysics and Medicine, University of California, San Francisco, CA 94143-2200, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1AB339Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IRE1ERN1
EC: 2.7.11.1 (UniProt), 3.1.26 (UniProt)
Find proteins for P32361 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32361 
Go to UniProtKB:  P32361
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptideD8N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.244 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.3α = 90
b = 103.3β = 90
c = 401.4γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance