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 
  • R-Value Observed: 0.251 

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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: https://doi.org/10.1126/science.1178705
  • Primary Citation of Related Structures:  
    3A6P

  • 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 triphosphate (GTP)-bound form of the small nuclear guanine triphosphatase (GTPase) Ran (RanGTP) ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exportin-5
A, F
1,204Homo sapiensMutation(s): 0 
Gene Names: XPO5, KIAA1291, RANBP21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAV4 (Homo sapiens)
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Go to UniProtKB:  Q9HAV4
PHAROS:  Q9HAV4
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UniProt GroupQ9HAV4
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
13-mer peptide
B, G
13Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran
C, H
216Canis lupus familiarisMutation(s): 0 
Gene Names: RAN
EC: 3.6.5
UniProt
Find proteins for P62825 (Canis lupus familiaris)
Explore P62825 
Go to UniProtKB:  P62825
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UniProt GroupP62825
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Entity ID: 4
MoleculeChainsLengthOrganismImage
pre-microRNA
D, I
24N/A
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Entity ID: 5
MoleculeChainsLengthOrganismImage
pre-microRNA
E, J
24N/A
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
K [auth C],
M [auth H]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
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L [auth C],
N [auth H]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.157α = 90
b = 304.667β = 110.79
c = 89.23γ = 90
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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