9OG9 | pdb_00009og9

Cryo-EM structure of human full-length XPO1 (unliganded)

• PDB DOI: https://doi.org/10.2210/pdb9OG9/pdb
• EM Map EMD-70458: EMDB EMDataResource

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-04-30 Released: 2025-11-26 
• Deposition Author(s): Wing, C.E., Fung, H.Y.J., Chook, Y.M.
• Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

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

• PubMed: 41286136 
• 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.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
KU Leuven Department of Microbiology, Immunology and Transplantation, Molecular Genetics and Therapeutics in Virology and Oncology Research Group, Rega Institute for Medical Research, Leuven Cancer Institute (LKI), Leuven, Belgium.
Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.
Department of Clinical, Diagnostic & Therapeutic Sciences, College of Allied Health Professions, University of Nebraska Medical Center, Omaha, NE, USA.
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Karyopharm Therapeutics, Inc., Newton, MA, USA.
Nexgen Biopharma Solutions, Inc., Brookline, MA, USA.
Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA. [e-mail].
KU Leuven Department of Microbiology, Immunology and Transplantation, Molecular Genetics and Therapeutics in Virology and Oncology Research Group, Rega Institute for Medical Research, Leuven Cancer Institute (LKI), Leuven, Belgium. [e-mail].
Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 123.66 kDa 
• Atom Count: 7,321 
• Modeled Residue Count: 902 
• Deposited Residue Count: 1,073 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-1	A	1,073	Homo sapiens	Mutation(s): 0  Gene Names: XPO1, CRM1
UniProt & NIH Common Fund Data Resources
Find proteins for O14980 (Homo sapiens) Explore O14980  Go to UniProtKB:  O14980
GTEx:  ENSG00000082898

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Wing, C.E., Fung, H.Y.J., Chook, Y.M.

---

Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP220582
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP180410
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP150053
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP170170
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM144137
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM131963
Welch Foundation	United States	I-1532

Revision History  

• 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