› 4hb4

X-ray diffraction
2.05Å resolution

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

Released:
DOI: 10.2210/pdb4hb4/pdb
PDB entry 4hb4 coloured by chain, front view.
PDB entry 4hb4 coloured by chain, side view.
PDB entry 4hb4 coloured by chain, top view.
Source organisms:
Primary publication:
Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1.
Sun Q, Carrasco YP, Hu Y, Guo X, Mirzaei H, Macmillan J, Chook YM
Proc Natl Acad Sci U S A 110 1303-8 (2013)
PMID: 23297231

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-542260 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
GTP-binding nuclear protein Ran Chain: A
Molecule details ›
Chain: A
Length: 216 amino acids
Theoretical weight: 24.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62826 (Residues: 1-216; Coverage: 100%)
Gene names: ARA24, OK/SW-cl.81, RAN
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases
Ran-specific GTPase-activating protein 1 Chain: B
Molecule details ›
Chain: B
Length: 140 amino acids
Theoretical weight: 16.38 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P41920 (Residues: 62-201; Coverage: 70%)
Gene names: CST20, HTN1, SFO1, YD8119.08, YDR002W, YRB1
Sequence domains: RanBP1 domain
Structure domains: Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Exportin-1 Chain: C
Molecule details ›
Chain: C
Length: 1023 amino acids
Theoretical weight: 117.37 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P30822 (Residues: 1-1058; Coverage: 94%)
Gene names: CRM1, G8514, KAP124, XPO1, YGR218W
Sequence domains:

Ligands and Environments

6 bound ligands:
Ligand GNP 1 x GNP
Ligand MG 1 x MG
Ligand EDO 2 x EDO
Ligand LMB 1 x LMB
Ligand GOL 1 x GOL
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P43212
Unit cell:
a: 105.97Å b: 105.97Å c: 304.934Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.188 0.218
Expression system: Escherichia coli

Quick links

Citations

27 review citations

Nucleo-cytoplasmic transport as a therapeutic target of cancer.
Gravina et al. (2014)
26 more

2 mentions without citation

Allosteric control of the exportin CRM1 unraveled by crystal structure analysis.
Monecke et al. (2014)
1 more