1I4D

CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways.

Tarricone, C.Xiao, B.Justin, N.Walker, P.A.Rittinger, K.Gamblin, S.J.Smerdon, S.J.

(2001) Nature 411: 215-219

  • DOI: 10.1038/35075620
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small G proteins are GTP-dependent molecular switches that regulate numerous cellular functions. They can be classified into homologous subfamilies that are broadly associated with specific biological processes. Cross-talk between small G-protein fam ...

    Small G proteins are GTP-dependent molecular switches that regulate numerous cellular functions. They can be classified into homologous subfamilies that are broadly associated with specific biological processes. Cross-talk between small G-protein families has an important role in signalling, but the mechanism by which it occurs is poorly understood. The coordinated action of Arf and Rho family GTPases is required to regulate many cellular processes including lipid signalling, cell motility and Golgi function. Arfaptin is a ubiquitously expressed protein implicated in mediating cross-talk between Rac (a member of the Rho family) and Arf small GTPases. Here we show that Arfaptin binds specifically to GTP-bound Arf1 and Arf6, but binds to Rac.GTP and Rac.GDP with similar affinities. The X-ray structure of Arfaptin reveals an elongated, crescent-shaped dimer of three-helix coiled-coils. Structures of Arfaptin with Rac bound to either GDP or the slowly hydrolysable analogue GMPPNP show that the switch regions adopt similar conformations in both complexes. Our data highlight fundamental differences between the molecular mechanisms of Rho and Ras family signalling, and suggest a model of Arfaptin-mediated synergy between the Arf and Rho family signalling pathways.


    Organizational Affiliation

    Division of Protein Structure, National Institute for Medical Research, Mill Hill, London NW7 IAA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ARFAPTIN 2
A, B
224Homo sapiensMutation(s): 0 
Gene Names: ARFIP2 (POR1)
Find proteins for P53365 (Homo sapiens)
Go to Gene View: ARFIP2
Go to UniProtKB:  P53365
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
D
192Homo sapiensMutation(s): 0 
Gene Names: RAC1 (TC25)
Find proteins for P63000 (Homo sapiens)
Go to Gene View: RAC1
Go to UniProtKB:  P63000
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GDPKd: 3000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.566α = 90.00
b = 47.462β = 97.51
c = 125.311γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Data collection