› 5dhf

X-ray diffraction
2.28Å resolution

Crystal Structure of hRio2 NES Peptide in complex with CRM1-Ran-RanBP1

Released:
DOI: 10.2210/pdb5dhf/pdb
PDB entry 5dhf coloured by chain, front view.
PDB entry 5dhf coloured by chain, side view.
PDB entry 5dhf coloured by chain, top view.
Source organisms:
Primary publication:
Structural determinants of nuclear export signal orientation in binding to exportin CRM1.
Fung HY, Fu SC, Brautigam CA, Chook YM
OpenAccess logo Elife 4 (2015)
PMID: 26349033

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-542266 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
GTP-binding nuclear protein Ran Chain: A
Molecule details ›
Chain: A
Length: 237 amino acids
Theoretical weight: 26.76 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: 143 amino acids
Theoretical weight: 16.52 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: 117.46 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:
Serine/threonine-protein kinase RIO2 Chain: D
Molecule details ›
Chain: D
Length: 19 amino acids
Theoretical weight: 2.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BVS4 (Residues: 389-403; Coverage: 3%)
Gene names: RIO2, RIOK2

Ligands and Environments

5 bound ligands:
Ligand GNP 1 x GNP
Ligand MG 1 x MG
Ligand GOL 4 x GOL
Ligand CL 2 x CL
Ligand ZN 1 x ZN
1 modified residue:
Ligand MSE 1 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P43212
Unit cell:
a: 106.479Å b: 106.479Å c: 303.731Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.178 0.218
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

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

3 mentions without citation

Impact of structural biology and the protein data bank on us fda new drug approvals of low molecular weight antineoplastic agents 2019-2023.
Burley et al. (2024)
2 more