1KSH

Complex of Arl2 and PDE delta, Crystal Form 2 (native)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The complex of Arl2-GTP and PDE delta: from structure to function.

Hanzal-Bayer, M.Renault, L.Roversi, P.Wittinghofer, A.Hillig, R.C.

(2002) EMBO J. 21: 2095-2106

  • DOI: 10.1093/emboj/21.9.2095
  • Primary Citation of Related Structures:  1KSG, 1KSJ

  • PubMed Abstract: 
  • Arf-like (Arl) proteins are close relatives of the Arf regulators of vesicular transport, but their function is unknown. Here, we present the crystal structure of full-length Arl2-GTP in complex with its effector PDE delta solved in two crystal forms ...

    Arf-like (Arl) proteins are close relatives of the Arf regulators of vesicular transport, but their function is unknown. Here, we present the crystal structure of full-length Arl2-GTP in complex with its effector PDE delta solved in two crystal forms (Protein Data Bank codes 1KSG, 1KSH and 1KSJ). Arl2 shows a dramatic conformational change from the GDP-bound form, which suggests that it is reversibly membrane associated. PDE delta is structurally closely related to RhoGDI and contains a deep empty hydrophobic pocket. Further experiments show that H-Ras, Rheb, Rho6 and G alpha(i1) interact with PDE delta and that, at least for H-Ras, the intact C-terminus is required. We suggest PDE delta to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE delta-mediated transport.


    Related Citations: 
    • Structural and biochemical properties show Arl3-GDP as a distinct GTP-binding protein
      Hillig, R.C.,Hanzal-Bayer, M.,Linari, M.,Becker, J.,Wittinghofer, A.,Renault, L.
      (2000) Structure 8: 1239
    • The delta subunit of rod specific cyclic GMP phosphodiesterase, PDE delta, interacts with the Arf-like protein Arl3 in a GTP specific manner
      Linari, M.,Hanzal-Bayer, M.,Becker, J.
      (1999) FEBS Lett. 458: 55
    • Coexpression, copurification, crystallization and preliminary X-ray analysis of a complex of Arl2-GTP and PDE delta
      Renault, L.,Hanzal-Bayer, M.,Hillig, R.C.
      (2001) Acta Crystallogr.,Sect.D 57: 1167


    Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Abteilung Strukturelle Biologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
arf-like protein 2
A
186Mus musculusGene Names: Arl2
Find proteins for Q9D0J4 (Mus musculus)
Go to UniProtKB:  Q9D0J4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE DELTA-SUBUNIT
B
152Homo sapiensGene Names: PDE6D (PDED)
Find proteins for O43924 (Homo sapiens)
Go to Gene View: PDE6D
Go to UniProtKB:  O43924
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.454α = 90.00
b = 65.395β = 90.00
c = 104.409γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
AMoREphasing
ARP/wARPmodel building
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance