1KSH

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

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Ligand Structure Quality Assessment 


This is version 1.3 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, 1KSH, 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 (Protein Data Bank codes 1KSG, 1KSH and 1KSJ) ...

    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: 
    • 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 D Biol Crystallogr 57: 1167
    • 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
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
arf-like protein 2A186Mus musculusMutation(s): 2 
Gene Names: Arl2
UniProt
Find proteins for Q9D0J4 (Mus musculus)
Explore Q9D0J4 
Go to UniProtKB:  Q9D0J4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D0J4
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE DELTA-SUBUNITB152Homo sapiensMutation(s): 1 
Gene Names: PDE6D or PDED, PDE6D, PDED
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for O43924 (Homo sapiens)
Explore O43924 
Go to UniProtKB:  O43924
PHAROS:  O43924
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43924
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME		A L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.454α = 90
b = 65.395β = 90
c = 104.409γ = 90
Software Package:
Software NamePurpose
AMoREphasing
ARP/wARPmodel building
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations