4C0A

Arf1(Delta1-17)in complex with BRAG2 Sec7-PH domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Integrated Conformational and Lipid-Sensing Regulation of Endosomal Arfgef Brag2.

Aizel, K.Biou, V.Navaza, J.Duarte, L.V.Campanacci, V.Cherfils, J.Zeghouf, M.

(2013) Plos Biol. 11: 01652

  • DOI: 10.1371/journal.pbio.1001652

  • PubMed Abstract: 
  • The mechanisms whereby guanine nucleotide exchange factors (GEFs) coordinate their subcellular targeting to their activation of small GTPases remain poorly understood. Here we analyzed how membranes control the efficiency of human BRAG2, an ArfGEF in ...

    The mechanisms whereby guanine nucleotide exchange factors (GEFs) coordinate their subcellular targeting to their activation of small GTPases remain poorly understood. Here we analyzed how membranes control the efficiency of human BRAG2, an ArfGEF involved in receptor endocytosis, Wnt signaling, and tumor invasion. The crystal structure of an Arf1-BRAG2 complex that mimics a membrane-bound intermediate revealed an atypical PH domain that is constitutively anchored to the catalytic Sec7 domain and interacts with Arf. Combined with the quantitative analysis of BRAG2 exchange activity reconstituted on membranes, we find that this PH domain potentiates nucleotide exchange by about 2,000-fold by cumulative conformational and membrane-targeting contributions. Furthermore, it restricts BRAG2 activity to negatively charged membranes without phosphoinositide specificity, using a positively charged surface peripheral to but excluding the canonical lipid-binding pocket. This suggests a model of BRAG2 regulation along the early endosomal pathway that expands the repertoire of GEF regulatory mechanisms. Notably, it departs from the auto-inhibitory and feedback loop paradigm emerging from studies of SOS and cytohesins. It also uncovers a novel mechanism of unspecific lipid-sensing by PH domains that may allow sustained binding to maturating membranes.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IQ MOTIF AND SEC7 DOMAIN-CONTAINING PROTEIN 1
A, B, E, F
383Homo sapiensMutation(s): 1 
Gene Names: IQSEC1 (ARFGEP100, BRAG2, KIAA0763)
Find proteins for Q6DN90 (Homo sapiens)
Go to Gene View: IQSEC1
Go to UniProtKB:  Q6DN90
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ADP-RIBOSYLATION FACTOR 1
C, D, G, H
164Bos taurusMutation(s): 0 
Gene Names: ARF1
Find proteins for P84080 (Bos taurus)
Go to Gene View: ARF1
Go to UniProtKB:  P84080
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G3D
Query on G3D

Download SDF File 
Download CCD File 
C, D, G, H
GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
C10 H16 N5 O14 P3
HEYSFDAMRDTCJM-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.980α = 90.00
b = 65.780β = 96.13
c = 196.860γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
AMoREphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Database references