1S9D

ARF1[DELTA 1-17]-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Snapshots of the Mechanism and Inhibition of a Guanine Nucleotide Exchange Factor

Renault, L.Guibert, B.Cherfils, J.

(2003) Nature 426: 525-530

  • DOI: 10.1038/nature02197
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small GTP-binding (G) proteins are activated by GDP/GTP nucleotide exchange stimulated by guanine nucleotide exchange factors (GEFs). Nucleotide dissociation from small G protein-GEF complexes involves transient GDP-bound intermediates whose structur ...

    Small GTP-binding (G) proteins are activated by GDP/GTP nucleotide exchange stimulated by guanine nucleotide exchange factors (GEFs). Nucleotide dissociation from small G protein-GEF complexes involves transient GDP-bound intermediates whose structures have never been described. In the case of Arf proteins, small G proteins that regulate membrane traffic in eukaryotic cells, such intermediates can be trapped either by the natural inhibitor brefeldin A or by charge reversal at the catalytic glutamate of the Sec7 domain of their GEFs. Here we report the crystal structures of these intermediates that show that membrane recruitment of Arf and nucleotide dissociation are separate reactions stimulated by Sec7. The reactions proceed through sequential rotations of the Arf.GDP core towards the Sec7 catalytic site, and are blocked by interfacial binding of brefeldin A and unproductive stabilization of GDP by charge reversal. The structural characteristics of the reaction and its modes of inhibition reveal unexplored ways in which to inhibit the activation of small G proteins.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR 9063, Avenue de la Terrasse, 91198 Gif sur Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-Ribosylation Factor 1
A
164Bos taurusMutation(s): 0 
Gene Names: ARF1
Find proteins for P84080 (Bos taurus)
Go to Gene View: ARF1
Go to UniProtKB:  P84080
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Arno
E
203Homo sapiensMutation(s): 4 
Gene Names: CYTH2 (ARNO, PSCD2, PSCD2L)
Find proteins for Q99418 (Homo sapiens)
Go to Gene View: CYTH2
Go to UniProtKB:  Q99418
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AFB
Query on AFB

Download SDF File 
Download CCD File 
A
1,6,7,8,9,11A,12,13,14,14A-DECAHYDRO-1,13-DIHYDROXY-6-METHYL-4H-CYCLOPENT[F]OXACYCLOTRIDECIN-4-ONE
BREFELDIN A
C16 H24 O4
KQNZDYYTLMIZCT-KQPMLPITSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
E
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.462α = 90.00
b = 111.462β = 90.00
c = 74.534γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
REFMACrefinement
XDSdata scaling
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description