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 

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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
  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-RIBOSYLATION FACTOR 6A, B, E165Homo sapiensMutation(s): 1 
Gene Names: ARF6
UniProt & NIH Common Fund Data Resources
Find proteins for P62330 (Homo sapiens)
Explore P62330 
Go to UniProtKB:  P62330
PHAROS:  P62330
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4C, D77Homo sapiensMutation(s): 0 
Gene Names: SPAG9HSSKIAA0516MAPK8IP4SYD1HLC6
UniProt & NIH Common Fund Data Resources
Find proteins for O60271 (Homo sapiens)
Explore O60271 
Go to UniProtKB:  O60271
PHAROS:  O60271
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
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
 Ligand Interaction
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A], K [auth B], O [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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 
  • 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

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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