6TVO

Human CRM1-RanGTP in complex with Leptomycin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Characterization of Inhibition Reveals Distinctive Properties for Human andSaccharomyces cerevisiaeCRM1.

Shaikhqasem, A.Dickmanns, A.Neumann, P.Ficner, R.

(2020) J Med Chem 63: 7545-7558

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00143
  • Primary Citation of Related Structures:  
    6TVO

  • PubMed Abstract: 

    The receptor CRM1 is responsible for the nuclear export of many tumor-suppressor proteins and viral ribonucleoproteins. This renders CRM1 an interesting target for therapeutic intervention in diverse cancer types and viral diseases. Structural studies of Saccharomyces cerevisiae CRM1 ( Sc CRM1) complexes with inhibitors defined the molecular basis for CRM1 inhibition. Nevertheless, no structural information is available for inhibitors bound to human CRM1 ( Hs CRM1). Here, we present the structure of the natural inhibitor Leptomycin B bound to the Hs CRM1-RanGTP complex. Despite high sequence conservation and structural similarity in the NES-binding cleft region, Sc CRM1 exhibits 16-fold lower binding affinity than Hs CRM1 toward PKI-NES and significant differences in affinities toward potential CRM1 inhibitors. In contrast to Hs CRM1, competition assays revealed that a human adapted mutant Sc CRM1-T539C does not bind all inhibitors tested. Taken together, our data indicate the importance of using Hs CRM1 for molecular analysis and development of novel antitumor and antiviral drugs.


  • Organizational Affiliation

    Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein RanA [auth B]182Homo sapiensMutation(s): 1 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-1B [auth A]1,060Homo sapiensMutation(s): 3 
Gene Names: XPO1CRM1
UniProt & NIH Common Fund Data Resources
Find proteins for O14980 (Homo sapiens)
Explore O14980 
Go to UniProtKB:  O14980
PHAROS:  O14980
GTEx:  ENSG00000082898 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14980
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.29α = 90
b = 151.33β = 90
c = 234.843γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2020-08-05
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description