› 6q84

X-ray diffraction
3.7Å resolution

Crystal structure of RanGTP-Pdr6-eIF5A export complex

Released:
DOI: 10.2210/pdb6q84/pdb
PDB entry 6q84 coloured by chain, front view.
PDB entry 6q84 coloured by chain, side view.
PDB entry 6q84 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122.
Aksu M, Trakhanov S, Vera Rodriguez A, Görlich D
OpenAccess logo J Cell Biol 218 1839-1852 (2019)
PMID: 31023722

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-149927 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Importin beta-like protein KAP122 Chains: A, D
Molecule details ›
Chains: A, D
Length: 1080 amino acids
Theoretical weight: 123.49 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P32767 (Residues: 2-1081; Coverage: 100%)
Gene names: KAP122, PDR6, YGL016W
GTP-binding nuclear protein Ran Chains: B, E
Molecule details ›
Chains: B, E
Length: 176 amino acids
Theoretical weight: 20.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62826 (Residues: 5-180; Coverage: 82%)
Gene names: ARA24, OK/SW-cl.81, RAN
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases
Eukaryotic translation initiation factor 5A-1 Chains: C, F
Molecule details ›
Chains: C, F
Length: 142 amino acids
Theoretical weight: 15.53 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P23301 (Residues: 16-157; Coverage: 90%)
Gene names: HYP2, SYGP-ORF21, TIF51A, YEL034W
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GTP 2 x GTP
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P63
Unit cell:
a: 139.54Å b: 139.54Å c: 346.57Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.227 0.206 0.247
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Karyopherin-mediated nucleocytoplasmic transport.
Wing et al. (2022)
4 more

2 mentions without citation

Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122.
Aksu et al. (2019)
1 more