5YU6

CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Selective Binding of Export Cargoes by Exportin-5

Yamazawa, R.Jiko, C.Choi, S.Park, I.Y.Nakagawa, A.Yamashita, E.Lee, S.J.

(2018) Structure 26: 1393-1398.e2

  • DOI: 10.1016/j.str.2018.06.014
  • Primary Citation of Related Structures:  
    5YU6, 5YU7

  • PubMed Abstract: 
  • In the nucleus, RanGTP binding to importin dissociates the cargo. On the other hand, RanGTP enables exportin to bind export cargo and form the export complex by each exportin's own cargo selection mechanism. Here, we present two X-ray structures for Exportin-5 (Exp-5) alone and Exp-5:RanGTP intermediate complex ...

    In the nucleus, RanGTP binding to importin dissociates the cargo. On the other hand, RanGTP enables exportin to bind export cargo and form the export complex by each exportin's own cargo selection mechanism. Here, we present two X-ray structures for Exportin-5 (Exp-5) alone and Exp-5:RanGTP intermediate complex. The structure of Exp-5 adopts a ring-shaped closed conformation by C-terminal anchor residues 1,167-1,179, interacting with N-terminal heat repeats 4-9. The closed form of Exp-5 is important for the stability of the cargo-free state. Interaction between Exp-5 and RanGTP induces elimination of intramolecular contacts of the C-terminal anchor. A large movement of N-terminal 1-9th heat repeats and C-terminal 19-20th heat repeats creates an open space for RanGTP accommodation. Exp-5 in Exp-5:RanGTP and Exp-5:RanGTP:pre-miRNA adopts the same conformation. RanGTP binding to Exp-5 creates a selective molecular cage area for accepting its cargoes, such as small double-stranded RNAs, without conformational change in Exp-5:RanGTP.


    Organizational Affiliation

    College of Pharmacy, Chungbuk National University, Osongseangmyung 1, Heungduk-gu, Cheongju, Chungbuk, Korea. Electronic address: sjlee@chungbuk.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exportin-5A, D [auth C]1204Homo sapiensMutation(s): 0 
Gene Names: XPO5KIAA1291RANBP21
Find proteins for Q9HAV4 (Homo sapiens)
Explore Q9HAV4 
Go to UniProtKB:  Q9HAV4
NIH Common Fund Data Resources
PHAROS:  Q9HAV4
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
13-mer peptideB [auth E], E [auth F]13unidentifiedMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein RanC [auth B], F [auth D]216Canis lupus familiarisMutation(s): 0 
Gene Names: RAN
Find proteins for P62825 (Canis lupus familiaris)
Explore P62825 
Go to UniProtKB:  P62825
Protein Feature View
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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 
G [auth B], I [auth D]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth B], J [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.56α = 90
b = 302.678β = 109.24
c = 88.264γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXTJapan22121006
JSPSJapan22370041
JSPSJapan21227003
NRFKorea, Republic OfMEST 2011-0017405

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-25
    Changes: Derived calculations