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 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: 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
GTEx:  ENSG00000178607 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75460
Sequence Annotations
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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
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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: ELOC, TCEB1
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
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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: ELOB, TCEB2
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
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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