1A2K

GDPRAN-NTF2 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran.

Stewart, M.Kent, H.M.McCoy, A.J.

(1998) J Mol Biol 277: 635-646

  • DOI: 10.1006/jmbi.1997.1602
  • Primary Citation of Related Structures:  
    5BXQ, 1A2K

  • PubMed Abstract: 
  • Nuclear transport factor 2 (NTF2) and the Ras-family GTPase Ran are two soluble components of the nuclear protein import machinery. NTF2 binds GDP-Ran selectively and this interaction is important for efficient nuclear protein import in vivo. We have ...

    Nuclear transport factor 2 (NTF2) and the Ras-family GTPase Ran are two soluble components of the nuclear protein import machinery. NTF2 binds GDP-Ran selectively and this interaction is important for efficient nuclear protein import in vivo. We have used X-ray crystallography to determine the structure of the macromolecular complex formed between GDP-Ran and nuclear transport factor 2 (NTF2) at 2.5 A resolution. The interaction interface involves primarily the putative switch II loop of Ran (residues 65 to 78) and the hydrophobic cavity and surrounding surface of NTF2. The major contribution to the interaction made by the switch II loop accounts for the ability of NTF2 to discriminate between GDP and GTP-bound forms of Ran. The aromatic side-chain of Ran Phe72 inserts into the NTF2 cavity and accounts for 22% of the surface area buried by the interaction interface, while salt bridges are formed between Lys71 and Arg76 of Ran with Asp92/Asp94 and Glu42 of NTF2, respectively. These salt bridges account for the inhibition of the Ran-NTF2 interaction by NTF2 mutants such as E42 K and D92/94N in which the negatively charged residues surrounding the cavity were altered. Because the interaction interface maintains the positions of key Ran residues involved in binding MgGDP, NTF2 binding may help stabilize the switch state of Ran, possibly in the context of targeting it to other components of the nuclear protein import machinery to specify directionality of transport. The binding of GDP-Ran at the NTF2 cavity raises the possibility that this interaction might be modulated by a metabolite or small molecule substrate for NTF2's putative enzymatic activity.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR TRANSPORT FACTOR 2AB127Rattus norvegicusMutation(s): 0 
Gene Names: Nutf2Ntf2
Find proteins for P61972 (Rattus norvegicus)
Explore P61972 
Go to UniProtKB:  P61972
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RANCDE216Canis 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download CCD File 
C, D, E
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.15α = 90
b = 120.54β = 90
c = 108.92γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance