9N88 | pdb_00009n88

PROTAC-induced IRE1 ternary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9N88

This is version 1.1 of the entry. See complete history

Literature

Chemically-induced degradation of the endoplasmic-reticulum stress sensor IRE1 by a VHL-recruiting chimera.

Du, J.Villemure, E.Johnson, M.Azumaya, C.Gaspar, C.J.Marsters, S.Lawrence, D.Foster, S.Rohou, A.Cheung, T.K.Rose, C.M.Garner, T.Ro, S.Clark, K.Beresini, M.H.Braun, M.G.Rudolph, J.Hsu, P.Ashkenazi, A.

(2025) Nat Commun 16: 11445-11445

  • DOI: https://doi.org/10.1038/s41467-025-66382-8
  • Primary Citation Related Structures: 
    9N88

  • PubMed Abstract: 

    The endoplasmic-reticulum (ER) transmembrane protein IRE1 mitigates ER stress through kinase-endoribonuclease and scaffolding activities. Cancer cells often co-opt IRE1 to facilitate growth. An IRE1-RNase inhibitor has entered clinical trials; however, recent work uncovered a significant nonenzymatic IRE1 dependency in cancer. To fully disrupt IRE1, we describe a proteolysis-targeting chimera (G6374) that couples an IRE1-kinase ligand to a compound that binds the ubiquitin Cullin-RING Ligase (CRL) substrate receptor, VHL. G6374 induces a stable, cooperative interaction between IRE1 and VHL, driving K48-linked ubiquitination on two principal lysine residues in the IRE1-kinase domain and inducing proteasomal IRE1 degradation. Cryogenic electron microscopy and mutagenesis studies reveal a 2:2 IRE1:VHL ternary-complex topology and critical interactional features, informing future designs. G6374 blocks growth of IRE1-dependent cancer cells irrespective of their dependency mode, while sparing IRE1-independent cells. We provide a proof-of-concept for VHL-based degradation of an ER-transmembrane protein, advancing strategies to fully disrupt IRE1.


  • Organizational Affiliation
    • Department of Research Oncology, Genentech, Inc., South San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 151.02 kDa 
  • Atom Count: 9,766 
  • Modeled Residue Count: 1,220 
  • Deposited Residue Count: 1,298 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1A,
C [auth E]
402Homo sapiensMutation(s): 0 
Gene Names: ERN1IRE1
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
GTEx:  ENSG00000178607 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75460
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressorB,
D [auth F]
147Homo sapiensMutation(s): 0 
Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens)
Explore P40337 
Go to UniProtKB:  P40337
PHAROS:  P40337
GTEx:  ENSG00000134086 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40337
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-CE [auth G],
F [auth C]
94Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15369
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-B peptideG [auth D],
H
6Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
Entity Groups
UniProt GroupQ15370
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BWF
(Subject of Investigation/LOI)

Query on A1BWF



Download:Ideal Coordinates CCD File
I [auth B],
J [auth F]
3-methyl-N-(5-{4-[(1r,4S)-4-{[7-oxo-8-(propan-2-yl)-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}cyclohexyl]piperazin-1-yl}pentanoyl)-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide
C47 H66 N10 O5 S
NLSUEDHTOMHRAG-AHPJQPEPSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.6

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Data collection, Database references