› 5ysu

X-ray diffraction
2.3Å resolution

Plumbagin in complex with CRM1-RanM189D-RanBP1

Released:
DOI: 10.2210/pdb5ysu/pdb
PDB entry 5ysu coloured by chain, front view.
PDB entry 5ysu coloured by chain, side view.
PDB entry 5ysu coloured by chain, top view.
Source organisms:
Entry authors: Sun Q, Zhang Y

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-151811 (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: 24.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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: 16.32 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
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: 1024 amino acids
Theoretical weight: 117.44 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P30822 (Residues: 1-1058; Coverage: 94%)
Gene names: CRM1, G8514, KAP124, XPO1, YGR218W
Sequence domains:

Ligands and Environments

6 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 1 x MG
Ligand CL 2 x CL
Ligand NO3 4 x NO3
Ligand F2X 2 x F2X
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P43212
Unit cell:
a: 105.063Å b: 105.063Å c: 306.534Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.22 0.257
Expression system: Escherichia coli BL21(DE3)

Quick links