4Z7H

Crystal structure of human IRE1 cytoplasmic kinase-RNase region - complex with imidazopyridine compound 3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Molecular mechanisms of human IRE1 activation through dimerization and ligand binding.

Joshi, A., Newbatt, Y., McAndrew, P.C., Stubbs, M., Burke, R., Richards, M.W., Bhatia, C., Caldwell, J.J., McHardy, T., Collins, I., Bayliss, R.

(2015) Oncotarget 6: 13019-13035

  • DOI: 10.18632/oncotarget.3864
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • IRE1 transduces the unfolded protein response by splicing XBP1 through its C-terminal cytoplasmic kinase-RNase region. IRE1 autophosphorylation is coupled to RNase activity through formation of a back-to-back dimer, although the conservation of the u ...

    IRE1 transduces the unfolded protein response by splicing XBP1 through its C-terminal cytoplasmic kinase-RNase region. IRE1 autophosphorylation is coupled to RNase activity through formation of a back-to-back dimer, although the conservation of the underlying molecular mechanism is not clear from existing structures. We have crystallized human IRE1 in a back-to-back conformation only previously seen for the yeast homologue. In our structure the kinase domain appears primed for catalysis but the RNase domains are disengaged. Structure-function analysis reveals that IRE1 is autoinhibited through a Tyr-down mechanism related to that found in the unrelated Ser/Thr protein kinase Nek7. We have developed a compound that potently inhibits human IRE1 kinase activity while stimulating XBP1 splicing. A crystal structure of the inhibitor bound to IRE1 shows an increased ordering of the kinase activation loop. The structures of hIRE in apo and ligand-bound forms are consistent with a previously proposed model of IRE1 regulation in which formation of a back-to-back dimer coupled to adoption of a kinase-active conformation drive RNase activation. The structures provide opportunities for structure-guided design of IRE1 inhibitors.

    Organizational Affiliation: 

    Department of Biochemistry, University of Leicester, Leicester, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase/endoribonuclease IRE1
A, B
416Homo sapiensMutation(s): 0 
Gene Names: ERN1 (IRE1)
Find proteins for O75460 (Homo sapiens)
Go to Gene View: ERN1
Go to UniProtKB:  O75460
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
4L5
Query on 4L5
Download SDF File 
Download CCD File 
A, B
2-methoxy-4-[6-(propan-2-ylamino)imidazo[1,2-b]pyridazin-3-yl]benzamide
C17 H19 N5 O2
IBZJJCFFBCEGPS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.678α = 90.00
b = 81.957β = 90.00
c = 168.682γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-04-07 
  • Released Date: 2015-05-27 
  • Deposition Author(s): Joshi, A., Bayliss, R.
Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC24461/A13231

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-07-01
    Type: Database references