1R8Q

FULL-LENGTH ARF1-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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:  
    1S9D, 1R8M, 1R8S, 1R8Q

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylation factor 1A, B181Bos taurusMutation(s): 0 
Gene Names: ARF1
Find proteins for P84080 (Bos taurus)
Explore P84080 
Go to UniProtKB:  P84080
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ArnoE, F203Homo sapiensMutation(s): 4 
Gene Names: PSCD2ARNOCYTH2PSCD2L
Find proteins for Q99418 (Homo sapiens)
Explore Q99418 
Go to UniProtKB:  Q99418
NIH Common Fund Data Resources
PHAROS  Q99418
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G3D
Query on G3D

Download CCD File 
A, B
GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
C10 H16 N5 O14 P3
HEYSFDAMRDTCJM-UUOKFMHZSA-N
 Ligand Interaction
AFB
Query on AFB

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A, B
1,6,7,8,9,11A,12,13,14,14A-DECAHYDRO-1,13-DIHYDROXY-6-METHYL-4H-CYCLOPENT[F]OXACYCLOTRIDECIN-4-ONE
C16 H24 O4
KQNZDYYTLMIZCT-KQPMLPITSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.081α = 90
b = 109.773β = 90
c = 118.326γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description