4HAZ

Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1(R543S,K548E,K579Q)-Ran-RanBP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1.

Sun, Q.Carrasco, Y.P.Hu, Y.Guo, X.Mirzaei, H.Macmillan, J.Chook, Y.M.

(2013) Proc Natl Acad Sci U S A 110: 1303-1308

  • DOI: 10.1073/pnas.1217203110
  • Primary Citation of Related Structures:  
    4HAU, 4HAV, 4HAW, 4HAX, 4HAY, 4HAZ, 4HB0, 4HB2, 4HB3, 4HB4

  • PubMed Abstract: 
  • The polyketide natural product Leptomycin B inhibits nuclear export mediated by the karyopherin protein chromosomal region maintenance 1 (CRM1). Here, we present 1.8- to 2.0-Å-resolution crystal structures of CRM1 bound to Leptomycin B and related inhibitors Anguinomycin A and Ratjadone A ...

    The polyketide natural product Leptomycin B inhibits nuclear export mediated by the karyopherin protein chromosomal region maintenance 1 (CRM1). Here, we present 1.8- to 2.0-Å-resolution crystal structures of CRM1 bound to Leptomycin B and related inhibitors Anguinomycin A and Ratjadone A. Structural and complementary chemical analyses reveal an unexpected mechanism of inhibition involving covalent conjugation and CRM1-mediated hydrolysis of the natural products' lactone rings. Furthermore, mutagenesis reveals the mechanism of hydrolysis by CRM1. The nuclear export signal (NES)-binding groove of CRM1 is able to drive a chemical reaction in addition to binding protein cargoes for transport through the nuclear pore complex.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran A216Homo sapiensMutation(s): 0 
Gene Names: RANARA24OK/SW-cl.81
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
NIH Common Fund Data Resources
PHAROS:  P62826
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein 1 B140Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YRB1CST20HTN1SFO1YDR002WYD8119.08
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41920 
Go to UniProtKB:  P41920
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exportin-1 C1023Saccharomyces cerevisiaeMutation(s): 5 
Gene Names: CRM1KAP124XPO1YGR218WG8514
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30822 
Go to UniProtKB:  P30822
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.82α = 90
b = 105.82β = 90
c = 305.231γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-09-27 
  • Released Date: 2013-01-09 
  • Deposition Author(s): Sun, Q., Chook, Y.M.

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references
  • Version 1.2: 2013-02-06
    Changes: Database references
  • Version 1.3: 2017-07-26
    Changes: Source and taxonomy