2J59

Crystal structure of the ARF1:ARHGAP21-ArfBD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Arf1-Mediated Recruitment of Arhgap21 to Golgi Membranes.

Menetrey, J.Perderiset, M.Cicolari, J.Dubois, T.El Khatib, N.El Khadali, F.Franco, M.Chavrier, P.Houdusse, A.

(2007) Embo J. 26: 1953

  • DOI: 10.1038/sj.emboj.7601634

  • PubMed Abstract: 
  • ARHGAP21 is a Rho family GTPase-activating protein (RhoGAP) that controls the Arp2/3 complex and F-actin dynamics at the Golgi complex by regulating the activity of the small GTPase Cdc42. ARHGAP21 is recruited to the Golgi by binding to another smal ...

    ARHGAP21 is a Rho family GTPase-activating protein (RhoGAP) that controls the Arp2/3 complex and F-actin dynamics at the Golgi complex by regulating the activity of the small GTPase Cdc42. ARHGAP21 is recruited to the Golgi by binding to another small GTPase, ARF1. Here, we present the crystal structure of the activated GTP-bound form of ARF1 in a complex with the Arf-binding domain (ArfBD) of ARHGAP21 at 2.1 A resolution. We show that ArfBD comprises a PH domain adjoining a C-terminal alpha helix, and that ARF1 interacts with both of these structural motifs through its switch regions and triggers structural rearrangement of the PH domain. We used site-directed mutagenesis to confirm that both the PH domain and the helical motif are essential for the binding of ArfBD to ARF1 and for its recruitment to the Golgi. Our data demonstrate that two well-known small GTPase-binding motifs, the PH domain and the alpha helical motif, can combine to create a novel mode of binding to Arfs.


    Related Citations: 
    • Improving Diffraction from 3A to 2A for a Complex between a Small Gtpase and its Effector by Analysis of Crystal Contacts and Use of Reverse Screening.
      Menetrey, J.,Perderiset, M.,Cicolari, J.,Houdusse, A.,Stura, E.A.
      (2007) Cryst. Growth Des. 7: 2140


    Organizational Affiliation

    Centre de Recherche, UMR 144, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-RIBOSYLATION FACTOR 1
A, B, C, D, E, F
166Mus musculusMutation(s): 1 
Gene Names: Arf1
Find proteins for P84078 (Mus musculus)
Go to UniProtKB:  P84078
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RHO-GTPASE ACTIVATING PROTEIN 10
M, N, O, P, Q, R
168Homo sapiensMutation(s): 0 
Gene Names: ARHGAP21 (ARHGAP10, KIAA1424)
Find proteins for Q5T5U3 (Homo sapiens)
Go to Gene View: ARHGAP21
Go to UniProtKB:  Q5T5U3
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
M, N, O, P, Q, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
C, E, O
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download SDF File 
Download CCD File 
A, B, F
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.636α = 90.00
b = 132.136β = 90.01
c = 146.283γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance