9OGF | pdb_00009ogf

Cryo-EM structure of human exportin-1 conjugated with KPT-UTSW1 and bound to human ASB8-ELOB/C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9OGF

This is version 1.2 of the entry. See complete history

Literature

SINE compounds activate exportin 1 degradation through an allosteric mechanism.

Wing, C.E.Fung, H.Y.J.Kwanten, B.Cagatay, T.Niesman, A.B.Jacquemyn, M.Gharghabi, M.Permentier, B.Shakya, B.Nandi, R.Ready, J.M.Kashyap, T.Shacham, S.Landesman, Y.Lapalombella, R.Daelemans, D.Chook, Y.M.

(2025) Nat Chem Biol 21: 2002-2013

  • DOI: https://doi.org/10.1038/s41589-025-02058-0
  • Primary Citation Related Structures: 
    9OG9, 9OGA, 9OGB, 9OGC, 9OGD, 9OGE, 9OGF, 9OGN, 9OGO

  • PubMed Abstract: 

    Overexpression of exportin 1 (XPO1/CRM1) in cancer cells mislocalizes numerous cancer-related nuclear export cargoes. Covalent selective inhibitors of nuclear export (SINEs), including the cancer drug selinexor, restore proper nuclear localization by blocking XPO1-cargo interaction. These inhibitors also induce XPO1 degradation through the Cullin-RING E3 ligase (CRL) substrate receptor ASB8. Here we present cryo-electron microscopy structures revealing ASB8 binding to a cryptic XPO1 site that is exposed upon SINE conjugation. Unlike typical molecular glue degraders that directly bridge CRLs and substrates, SINEs bind XPO1 independently of ASB8, triggering an allosteric mechanism that enables high-affinity ASB8 recruitment, leading to XPO1 ubiquitination and degradation. ASB8-mediated degradation is also triggered by the endogenous itaconate derivative 4-octyl itaconate, suggesting that synthetic XPO1 inhibitors exploit a native cellular mechanism. This allosteric XPO1 degradation mechanism expands known modes of targeted protein degradation beyond molecular glue degraders and proteolysis-targeting chimeras of CRL4.


  • Organizational Affiliation
    • Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 177.91 kDa 
  • Atom Count: 7,738 
  • Modeled Residue Count: 964 
  • Deposited Residue Count: 1,562 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Exportin-11,073Homo sapiensMutation(s): 0 
Gene Names: XPO1CRM1
UniProt & NIH Common Fund Data Resources
Find proteins for O14980 (Homo sapiens)
Explore O14980 
Go to UniProtKB:  O14980
GTEx:  ENSG00000082898 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14980
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ankyrin repeat and SOCS box protein 8274Homo sapiensMutation(s): 0 
Gene Names: ASB8PP14212
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H765 (Homo sapiens)
Explore Q9H765 
Go to UniProtKB:  Q9H765
GTEx:  ENSG00000177981 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H765
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-CC [auth E]97Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  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:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-BD [auth F]118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
GTEx:  ENSG00000103363 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15370
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CBB
(Subject of Investigation/LOI)

Query on A1CBB



Download:Ideal Coordinates CCD File
E [auth A]propan-2-yl 3-(3-phenyl-1H-1,2,4-triazol-1-yl)propanoate
C14 H17 N3 O2
SHWWXNADDRIENT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP220582
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP180410
Cancer Prevention and Research Institute of Texas (CPRIT)United States150053
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP170170
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM144137
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM131963
Welch FoundationUnited StatesI-1532

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references
  • Version 1.2: 2026-07-22
    Changes: Data collection, Database references