4HAU

Crystal structure of CRM1 inhibitor Ratjadone A in complex with CRM1-Ran-RanBP1

• PDB DOI: https://doi.org/10.2210/pdb4HAU/pdb

• Classification: PROTEIN TRANSPORT/ANTIBIOTIC
• Organism(s): Homo sapiens, Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.148 
• R-Value Observed: 0.151 

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

• PubMed: 23297231 
• DOI: https://doi.org/10.1073/pnas.1217203110
• Primary Citation of Related Structures:  
  4HAT, 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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 159.87 kDa 
• Atom Count: 12,576 
• Modelled Residue Count: 1,334 
• Deposited Residue Count: 1,379 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	A	216	Homo sapiens	Mutation(s): 0  Gene Names: RAN, ARA24, OK/SW-cl.81 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens) Explore P62826  Go to UniProtKB:  P62826
PHAROS:  P62826 GTEx:  ENSG00000132341

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ran-specific GTPase-activating protein 1	B	140	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41920  Go to UniProtKB:  P41920

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-1	C	1,023	Saccharomyces cerevisiae	Mutation(s): 2  Gene Names: CRM1, KAP124, XPO1, YGR218W, G8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30822  Go to UniProtKB:  P30822

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
RJA	H [auth C]	Ratjadone A, bound form C28 H44 O6 SSWVBXXPYARFKL-PUAIALDQSA-N
GOL	I [auth C], J [auth C], K [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], L [auth C], M [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	N [auth C], O [auth C], P [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.148 
• R-Value Observed: 0.151 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.177	α = 90
b = 106.177	β = 90
c = 306.017	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2013-02-06
  Changes: Database references
• Version 1.3: 2017-07-26
  Changes: Source and taxonomy
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary