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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/emboj.2009.209

  • 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. ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-RIBOSYLATION FACTOR 6
A, B, E
165Homo sapiensMutation(s): 1 
Gene Names: ARF6
Find proteins for P62330 (Homo sapiens)
Go to Gene View: ARF6
Go to UniProtKB:  P62330
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4
C, D
77Homo sapiensMutation(s): 0 
Gene Names: SPAG9 (HSS, KIAA0516, MAPK8IP4, SYD1)
Find proteins for O60271 (Homo sapiens)
Go to Gene View: SPAG9
Go to UniProtKB:  O60271
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B, E
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
A, C, E
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.214 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 137.270α = 90.00
b = 137.270β = 90.00
c = 165.030γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance