3TJZ

Crystal Structure of Arf1 Bound to the gamma/zeta-COP Core Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A structure-based mechanism for arf1-dependent recruitment of coatomer to membranes.

Yu, X.Breitman, M.Goldberg, J.

(2012) Cell 148: 530-542

  • DOI: 10.1016/j.cell.2012.01.015

  • PubMed Abstract: 
  • Budding of COPI-coated vesicles from Golgi membranes requires an Arf family G protein and the coatomer complex recruited from cytosol. Arf is also required with coatomer-related clathrin adaptor complexes to bud vesicles from the trans-Golgi network ...

    Budding of COPI-coated vesicles from Golgi membranes requires an Arf family G protein and the coatomer complex recruited from cytosol. Arf is also required with coatomer-related clathrin adaptor complexes to bud vesicles from the trans-Golgi network and endosomal compartments. To understand the structural basis for Arf-dependent recruitment of a vesicular coat to the membrane, we determined the structure of Arf1 bound to the γζ-COP subcomplex of coatomer. Structure-guided biochemical analysis reveals that a second Arf1-GTP molecule binds to βδ-COP at a site common to the γ- and β-COP subunits. The Arf1-binding sites on coatomer are spatially related to PtdIns4,5P(2)-binding sites on the endocytic AP2 complex, providing evidence that the orientation of membrane binding is general for this class of vesicular coat proteins. A bivalent GTP-dependent binding mode has implications for the dynamics of coatomer interaction with the Golgi and for the selection of cargo molecules.


    Organizational Affiliation

    Howard Hughes Medical Institute and the Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosylation factor 1
A, D
164Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARF1
Find proteins for P11076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ARF1
Go to UniProtKB:  P11076
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit gamma
B, E
355Bos taurusMutation(s): 0 
Gene Names: COPG1 (COPG)
Find proteins for P53620 (Bos taurus)
Go to Gene View: COPG1
Go to UniProtKB:  P53620
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit zeta-1
C, F
153Bos taurusMutation(s): 0 
Gene Names: COPZ1 (COPZ)
Find proteins for P35604 (Bos taurus)
Go to Gene View: COPZ1
Go to UniProtKB:  P35604
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 163.579α = 90.00
b = 163.579β = 90.00
c = 145.188γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
PHENIXmodel building
CBASSdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release