6W3C

Structure of phosphorylated apo IRE1

• PDB DOI:  https://doi.org/10.2210/pdb6W3C/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-03-09 Released: 2020-12-09 
• Deposition Author(s): Wallweber, H., Mortara, K., Ferri, E., Wang, W., Rudolph, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.248 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Activation of the IRE1 RNase through remodeling of the kinase front pocket by ATP-competitive ligands.

Ferri, E., Le Thomas, A., Wallweber, H.A., Day, E.S., Walters, B.T., Kaufman, S.E., Braun, M.G., Clark, K.R., Beresini, M.H., Mortara, K., Chen, Y.A., Canter, B., Phung, W., Liu, P.S., Lammens, A., Ashkenazi, A., Rudolph, J., Wang, W.

(2020) Nat Commun 11: 6387-6387

• PubMed: 33318494 
• DOI: https://doi.org/10.1038/s41467-020-19974-5
• Primary Citation of Related Structures:  
  6W39, 6W3A, 6W3B, 6W3C, 6W3E, 6W3K


• PubMed Abstract: 
  

Inositol-Requiring Enzyme 1 (IRE1) is an essential component of the Unfolded Protein Response. IRE1 spans the endoplasmic reticulum membrane, comprising a sensory lumenal domain, and tandem kinase and endoribonuclease (RNase) cytoplasmic domains. Excess unfolded proteins in the ER lumen induce dimerization and oligomerization of IRE1, triggering kinase trans-autophosphorylation and RNase activation. Known ATP-competitive small-molecule IRE1 kinase inhibitors either allosterically disrupt or stabilize the active dimeric unit, accordingly inhibiting or stimulating RNase activity. Previous allosteric RNase activators display poor selectivity and/or weak cellular activity. In this study, we describe a class of ATP-competitive RNase activators possessing high selectivity and strong cellular activity. This class of activators binds IRE1 in the kinase front pocket, leading to a distinct conformation of the activation loop. Our findings reveal exquisitely precise interdomain regulation within IRE1, advancing the mechanistic understanding of this important enzyme and its investigation as a potential small-molecule therapeutic target.

---

Organizational Affiliation: 

Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 199.21 kDa 
• Atom Count: 13,478 
• Modelled Residue Count: 1,617 
• Deposited Residue Count: 1,736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase/endoribonuclease IRE1	A, B, C, D	434	Homo sapiens	Mutation(s): 0  Gene Names: ERN1, IRE1 EC: 2.7.11.1 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O75460 (Homo sapiens) Explore O75460  Go to UniProtKB:  O75460
PHAROS:  O75460

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B, C, D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.248 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.492	α = 90
b = 158.664	β = 91.01
c = 155.944	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Wallweber, H., Mortara, K., Ferri, E., Wang, W., Rudolph, J.

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Database references