› 3a6p

X-ray diffraction
2.92Å resolution

Crystal structure of Exportin-5:RanGTP:pre-miRNA complex

Released:
DOI: 10.2210/pdb3a6p/pdb
PDB entry 3a6p coloured by chain, front view.
PDB entry 3a6p coloured by chain, side view.
PDB entry 3a6p coloured by chain, top view.
Source organisms:
Primary publication:
A high-resolution structure of the pre-microRNA nuclear export machinery.
Okada C, Yamashita E, Lee SJ, Shibata S, Katahira J, Nakagawa A, Yoneda Y, Tsukihara T
Science 326 1275-9 (2009)
PMID: 19965479

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-158714 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
Exportin-5 Chains: A, F
Molecule details ›
Chains: A, F
Length: 1204 amino acids
Theoretical weight: 136.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HAV4 (Residues: 1-1204; Coverage: 100%)
Gene names: KIAA1291, RANBP21, XPO5
Sequence domains:
Structure domains: Leucine-rich Repeat Variant
13-mer peptide Chains: B, G
Molecule details ›
Chains: B, G
Length: 13 amino acids
Theoretical weight: 1.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
GTP-binding nuclear protein Ran Chains: C, H
Molecule details ›
Chains: C, H
Length: 216 amino acids
Theoretical weight: 24.46 KDa
Source organism: Canis lupus familiaris
Expression system: Escherichia coli
UniProt:
  • Canonical: P62825 (Residues: 1-216; Coverage: 100%)
Gene name: RAN
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases
pre-microRNA Chains: D, I
Molecule details ›
Chains: D, I
Length: 24 nucleotides
Theoretical weight: 7.69 KDa
pre-microRNA Chains: E, J
Molecule details ›
Chains: E, J
Length: 24 nucleotides
Theoretical weight: 7.66 KDa

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: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 71.157Å b: 304.667Å c: 89.23Å
α: 90° β: 110.79° γ: 90°
R-values:
R R work R free
0.251 0.247 0.312
Expression system: Escherichia coli

Quick links

Citations

129 review citations

Regulation of microRNA biogenesis.
Ha et al. (2014)
128 more

16 mentions without citation

Biogenesis and mechanism of action of small non-coding RNAs: insights from the point of view of structural biology.
Costa et al. (2012)
15 more