3A6P

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A high-resolution structure of the pre-microRNA nuclear export machinery

Okada, C.Yamashita, E.Lee, S.J.Shibata, S.Katahira, J.Nakagawa, A.Yoneda, Y.Tsukihara, T.

(2009) Science 326: 1275-1279

  • DOI: 10.1126/science.1178705

  • PubMed Abstract: 
  • Nuclear export of microRNAs (miRNAs) by exportin-5 (Exp-5) is an essential step in miRNA biogenesis. Here, we present the 2.9 angstrom structure of the pre-miRNA nuclear export machinery formed by pre-miRNA complexed with Exp-5 and a guanine triphosp ...

    Nuclear export of microRNAs (miRNAs) by exportin-5 (Exp-5) is an essential step in miRNA biogenesis. Here, we present the 2.9 angstrom structure of the pre-miRNA nuclear export machinery formed by pre-miRNA complexed with Exp-5 and a guanine triphosphate (GTP)-bound form of the small nuclear guanine triphosphatase (GTPase) Ran (RanGTP). The x-ray structure shows that Exp-5:RanGTP recognizes the 2-nucleotide 3' overhang structure and the double-stranded stem of the pre-miRNA. Exp-5:RanGTP shields the pre-miRNA stem from degradation in a baseball mitt-like structure where it is held by broadly distributed weak interactions, whereas a tunnel-like structure of Exp-5 interacts strongly with the 2-nucleotide 3' overhang through hydrogen bonds and ionic interactions. RNA recognition by Exp-5:RanGTP does not depend on RNA sequence, implying that Exp-5:RanGTP can recognize a variety of pre-miRNAs.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exportin-5
A, F
1204Homo sapiensGene Names: XPO5 (KIAA1291, RANBP21)
Find proteins for Q9HAV4 (Homo sapiens)
Go to Gene View: XPO5
Go to UniProtKB:  Q9HAV4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
13-mer peptide
B, G
13N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GTP-binding nuclear protein Ran
C, H
216Canis lupus familiarisGene Names: RAN
Find proteins for P62825 (Canis lupus familiaris)
Go to Gene View: RAN
Go to UniProtKB:  P62825
Entity ID: 4
MoleculeChainsLengthOrganism
pre-microRNAD,I24N/A
Entity ID: 5
MoleculeChainsLengthOrganism
pre-microRNAE,J24N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
C, H
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B, G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.157α = 90.00
b = 304.667β = 110.79
c = 89.230γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHARPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-04-25
    Type: Database references