7L5E

Crystal Structure of KPT-330 bound to CRM1 (537-DLTVK-541 to GLCEQ)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Recurrent XPO1 mutations alter pathogenesis of chronic lymphocytic leukemia.

Walker, J.S.Hing, Z.A.Harrington, B.Baumhardt, J.Ozer, H.G.Lehman, A.Giacopelli, B.Beaver, L.Williams, K.Skinner, J.N.Cempre, C.B.Sun, Q.Shacham, S.Stromberg, B.R.Summers, M.K.Abruzzo, L.V.Rassenti, L.Kipps, T.J.Parikh, S.Kay, N.E.Rogers, K.A.Woyach, J.A.Coppola, V.Chook, Y.M.Oakes, C.Byrd, J.C.Lapalombella, R.

(2021) J Hematol Oncol 14: 17-17

  • DOI: https://doi.org/10.1186/s13045-021-01032-2
  • Primary Citation of Related Structures:  
    6XJP, 6XJR, 6XJS, 6XJT, 6XJU, 7L5E

  • PubMed Abstract: 

    Exportin 1 (XPO1/CRM1) is a key mediator of nuclear export with relevance to multiple cancers, including chronic lymphocytic leukemia (CLL). Whole exome sequencing has identified hot-spot somatic XPO1 point mutations which we found to disrupt highly conserved biophysical interactions in the NES-binding groove, conferring novel cargo-binding abilities and forcing cellular mis-localization of critical regulators. However, the pathogenic role played by change-in-function XPO1 mutations in CLL is not fully understood.


  • Organizational Affiliation

    Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran216Homo sapiensMutation(s): 0 
Gene Names: RANARA24OK/SW-cl.81
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
PHAROS:  P62826
GTEx:  ENSG00000132341 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62826
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein 1140Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YRB1CST20HTN1SFO1YDR002WYD8119.08
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41920 
Go to UniProtKB:  P41920
Entity Groups  
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UniProt GroupP41920
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-11,024Saccharomyces cerevisiaeMutation(s): 4 
Gene Names: CRM1KAP124XPO1YGR218WG8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30822 
Go to UniProtKB:  P30822
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30822
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.434α = 90
b = 105.434β = 90
c = 305.08γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description