5NLY

Brag2 Sec7-PH (390-763), P212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Multiple interactions between an Arf/GEF complex and charged lipids determine activation kinetics on the membrane.

Karandur, D.Nawrotek, A.Kuriyan, J.Cherfils, J.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 11416-11421

  • DOI: 10.1073/pnas.1707970114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipidated small GTPases and their regulators need to bind to membranes to propagate actions in the cell, but an integrated understanding of how the lipid bilayer exerts its effect has remained elusive. Here we focused on ADP ribosylation factor (Arf) ...

    Lipidated small GTPases and their regulators need to bind to membranes to propagate actions in the cell, but an integrated understanding of how the lipid bilayer exerts its effect has remained elusive. Here we focused on ADP ribosylation factor (Arf) GTPases, which orchestrate a variety of regulatory functions in lipid and membrane trafficking, and their activation by the guanine-nucleotide exchange factor (GEF) Brag2, which controls integrin endocytosis and cell adhesion and is impaired in cancer and developmental diseases. Biochemical and structural data are available that showed the exceptional efficiency of Arf activation by Brag2 on membranes. We determined the high-resolution crystal structure of unbound Brag2 containing the GEF (Sec7) and membrane-binding (pleckstrin homology) domains, revealing that it has a constitutively active conformation. We used this structure to analyze the interaction of uncomplexed Brag2 and of the myristoylated Arf1/Brag2 complex with a phosphatidylinositol bisphosphate (PIP 2 ) -containing lipid bilayer, using coarse-grained molecular dynamics. These simulations revealed that the system forms a close-packed, oriented interaction with the membrane, in which multiple PIP 2 lipids bind the canonical lipid-binding site and unique peripheral sites of the PH domain, the Arf GTPase and, unexpectedly, the Sec7 domain. We cross-validated these predictions by reconstituting the binding and kinetics of Arf and Brag2 in artificial membranes. Our coarse-grained structural model thus suggests that the high efficiency of Brag2 requires interaction with multiple lipids and a well-defined orientation on the membrane, resulting in a local PIP 2 enrichment, which has the potential to signal toward the Arf pathway.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Cachan 94235, France; kuriyan@berkeley.edu jacqueline.cherfils@ens-paris-saclay.fr.,Ecole Normale Supérieure Paris-Saclay, Cachan 94235, France.,Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Cachan 94235, France.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; kuriyan@berkeley.edu jacqueline.cherfils@ens-paris-saclay.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IQ motif and SEC7 domain-containing protein 1
A
405Homo sapiensMutation(s): 0 
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
IQ motif and SEC7 domain-containing protein 1
B
405Homo sapiensMutation(s): 0 
Gene Names: IQSEC1 (ARFGEP100, BRAG2, KIAA0763)
Find proteins for Q6DN90 (Homo sapiens)
Go to Gene View: IQSEC1
Go to UniProtKB:  Q6DN90
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.893α = 90.00
b = 66.039β = 90.00
c = 206.880γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references