› 5yst

X-ray diffraction
2.04Å resolution

RanM189D in complex with RanBP1-CRM1

Released:
DOI: 10.2210/pdb5yst/pdb
PDB entry 5yst coloured by chain, front view.
PDB entry 5yst coloured by chain, side view.
PDB entry 5yst 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: 139 amino acids
Theoretical weight: 16.25 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P41920 (Residues: 62-200; Coverage: 69%)
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: 1017 amino acids
Theoretical weight: 116.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P30822 (Residues: 1-1052; Coverage: 94%)
Gene names: CRM1, G8514, KAP124, XPO1, YGR218W
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 2 x MG
Ligand EDO 1 x EDO
Ligand CL 6 x CL
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P43212
Unit cell:
a: 104.884Å b: 104.884Å c: 307.822Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.209 0.238
Expression system: Escherichia coli BL21(DE3)

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