› 1k5d

X-ray diffraction
2.7Å resolution

Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex

Released:
DOI: 10.2210/pdb1k5d/pdb
PDB entry 1k5d coloured by chain, front view.
PDB entry 1k5d coloured by chain, side view.
PDB entry 1k5d coloured by chain, top view.
Source organisms:
Primary publication:
RanGAP mediates GTP hydrolysis without an arginine finger.
Seewald MJ, Körner C, Wittinghofer A, Vetter IR
Nature 415 662-6 (2002)
PMID: 11832950

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-154391 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
GTP-binding nuclear protein Ran Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 216 amino acids
Theoretical weight: 24.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
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 Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 201 amino acids
Theoretical weight: 23.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P43487 (Residues: 1-201; Coverage: 100%)
Gene name: RANBP1
Sequence domains: RanBP1 domain
Structure domains: Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Ran GTPase-activating protein 1 Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 386 amino acids
Theoretical weight: 43.27 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Escherichia coli
UniProt:
  • Canonical: P41391 (Residues: 1-386; Coverage: 100%)
Gene names: SPAC22E12.07, rna1
Structure domains: Ribonuclease Inhibitor

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand GNP 4 x GNP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID13
Spacegroup: P1
Unit cell:
a: 101.551Å b: 103.109Å c: 120.177Å
α: 71.59° β: 80.55° γ: 67.78°
R-values:
R R work R free
0.24 0.237 0.267
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli

Quick links

Citations

31 review citations

GEFs and GAPs: critical elements in the control of small G proteins.
Bos et al. (2007)
30 more

25 mentions without citation

Transportin-1: A Nuclear Import Receptor with Moonlighting Functions.
Mboukou et al. (2021)
24 more