4HB4

Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1(537DLTVK541/GLCEQ)-Ran-RanBP1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 

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.USA 110: 1303-1308

  • DOI: 10.1073/pnas.1217203110
  • Primary Citation of Related Structures:  

  • 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 in ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-binding nuclear protein Ran
A
216Homo sapiensMutation(s): 0 
Gene Names: RAN (ARA24)
Find proteins for P62826 (Homo sapiens)
Go to Gene View: RAN
Go to UniProtKB:  P62826
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ran-specific GTPase-activating protein 1
B
140Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YRB1 (CST20, HTN1, SFO1)
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41920
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exportin-1
C
1023Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 5 
Gene Names: CRM1 (KAP124, XPO1)
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30822
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMB
Query on LMB
Download SDF File 
Download CCD File 
C
Leptomycin B, bound form
C33 H52 O7
GCBBLAVMGONVHO-XYERBDPFSA-N
 Ligand Interaction
CL
Query on CL
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Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
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Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
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Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP
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A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.970α = 90.00
b = 105.970β = 90.00
c = 304.934γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History 

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