4DCN

Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex with ARL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for membrane binding specificity of the Bin/Amphiphysin/Rvs (BAR) domain of Arfaptin-2 determined by Arl1 GTPase

Nakamura, K.Man, Z.Xie, Y.Hanai, A.Makyio, H.Kawasaki, M.Kato, R.Shin, H.-W.Nakayama, K.Wakatsuki, S.

(2012) J.Biol.Chem. 287: 25478-25489

  • DOI: 10.1074/jbc.M112.365783

  • PubMed Abstract: 
  • Membrane-sculpting BAR (Bin/Amphiphysin/Rvs) domains form a crescent-shaped homodimer that can sense and induce membrane curvature through its positively charged concave face. We have recently shown that Arfaptin-2, which was originally identified as ...

    Membrane-sculpting BAR (Bin/Amphiphysin/Rvs) domains form a crescent-shaped homodimer that can sense and induce membrane curvature through its positively charged concave face. We have recently shown that Arfaptin-2, which was originally identified as a binding partner for the Arf and Rac1 GTPases, binds to Arl1 through its BAR domain and is recruited onto Golgi membranes. There, Arfaptin-2 induces membrane tubules. Here, we report the crystal structure of the Arfaptin-2 BAR homodimer in complex with two Arl1 molecules bound symmetrically to each side, leaving the concave face open for membrane association. The overall structure of the Arl1·Arfaptin-2 BAR complex closely resembles that of the PX-BAR domain of sorting nexin 9, suggesting similar mechanisms underlying BAR domain targeting to specific organellar membranes. The Arl1·Arfaptin-2 BAR structure suggests that one of the two Arl1 molecules competes with Rac1, which binds to the concave face of the Arfaptin-2 BAR homodimer and may hinder its membrane association.


    Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, KEK, Tsukuba, Ibaraki 305-0801, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosylation factor-like protein 1
A, B
166Homo sapiensMutation(s): 1 
Gene Names: ARL1
Find proteins for P40616 (Homo sapiens)
Go to Gene View: ARL1
Go to UniProtKB:  P40616
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Arfaptin-2
C, D
198Homo sapiensMutation(s): 0 
Gene Names: ARFIP2 (POR1)
Find proteins for P53365 (Homo sapiens)
Go to Gene View: ARFIP2
Go to UniProtKB:  P53365
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.764α = 90.00
b = 111.125β = 90.00
c = 119.809γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references