2W83

Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Structural Basis of Arf Effector Specificity: The Crystal Structure of Arf6 in a Complex with Jip4.

Isabet, T.Montagnac, G.Regazzoni, K.Raynal, B.El Khadali, F.England, P.Franco, M.Chavrier, P.Houdusse, A.Menetrey, J.

(2009) EMBO J 28: 2835

  • DOI: https://doi.org/10.1038/emboj.2009.209
  • Primary Citation of Related Structures:  
    2W83

  • PubMed Abstract: 

    The JNK-interacting proteins, JIP3 and JIP4, are specific effectors of the small GTP-binding protein ARF6. The interaction of ARF6-GTP with the second leucine zipper (LZII) domains of JIP3/JIP4 regulates the binding of JIPs to kinesin-1 and dynactin. Here, we report the crystal structure of ARF6-GTP bound to the JIP4-LZII at 1.9 A resolution. The complex is a heterotetramer with dyad symmetry arranged in an ARF6-(JIP4)(2)-ARF6 configuration. Comparison of the ARF6-JIP4 interface with the equivalent region of ARF1 shows the structural basis of JIP4's specificity for ARF6. Using site-directed mutagenesis and surface plasmon resonance, we further show that non-conserved residues at the switch region borders are the key structural determinants of JIP4 specificity. A structure-derived model of the association of the ARF6-JIP3/JIP4 complex with membranes shows that the JIP4-LZII coiled-coil should lie along the membrane to prevent steric hindrances, resulting in only one ARF6 molecule bound. Such a heterotrimeric complex gives insights to better understand the ARF6-mediated motor switch regulatory function.


  • Organizational Affiliation

    Institut Curie, Centre de Recherche, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-RIBOSYLATION FACTOR 6
A, B, E
165Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P62330 (Homo sapiens)
Explore P62330 
Go to UniProtKB:  P62330
PHAROS:  P62330
GTEx:  ENSG00000165527 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62330
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4
C, D
77Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60271 (Homo sapiens)
Explore O60271 
Go to UniProtKB:  O60271
PHAROS:  O60271
GTEx:  ENSG00000008294 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60271
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth E]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO
Query on DIO

Download Ideal Coordinates CCD File 
H [auth A]
L [auth C]
M [auth C]
P [auth E]
Q [auth E]
H [auth A],
L [auth C],
M [auth C],
P [auth E],
Q [auth E],
R [auth E]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.27α = 90
b = 137.27β = 90
c = 165.03γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description