3BH7

Crystal structure of the RP2-Arl3 complex bound to GDP-AlF4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

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This is version 1.2 of the entry. See complete history


Literature

The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3

Veltel, S.Gasper, R.Eisenacher, E.Wittinghofer, A.

(2008) Nat Struct Mol Biol 15: 373-380

  • DOI: 10.1038/nsmb.1396
  • Primary Citation of Related Structures:  
    3BH6, 3BH7

  • PubMed Abstract: 
  • The retinitis pigmentosa 2 (RP2) gene is responsible for a particular variant of X chromosome-linked eye disease. Previously, RP2 was shown to bind the GTP form of the small G protein Arf-like 3 (Arl3), thus qualifying as an effector. Here we present the Arl3-GppNHp-RP2 complex structure, which shows features resembling complexes with GTPase-activating proteins (GAPs) ...

    The retinitis pigmentosa 2 (RP2) gene is responsible for a particular variant of X chromosome-linked eye disease. Previously, RP2 was shown to bind the GTP form of the small G protein Arf-like 3 (Arl3), thus qualifying as an effector. Here we present the Arl3-GppNHp-RP2 complex structure, which shows features resembling complexes with GTPase-activating proteins (GAPs). Biochemical analysis showing a 90,000-fold stimulation of the GTPase reaction together with the structure of an Arl3-GDP-AlF4--RP2 transition state complex showed that RP2 is an efficient GAP for Arl3, with structural features similar to other GAPs. Furthermore, the effect of mutations in patients with retinitis pigmentosa correlated with their effect on catalysis, in particular the mutation of the arginine finger of RP2. The cognate G protein-GAP pair is conserved in yeast as Cin4-Cin2, and the ability of RP2 to act as a GAP can be correlated with its ability to complement a CIN2-deletion phenotype.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylation factor-like protein 3A164Mus musculusMutation(s): 0 
Gene Names: Arl3
UniProt
Find proteins for Q9WUL7 (Mus musculus)
Explore Q9WUL7 
Go to UniProtKB:  Q9WUL7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein XRP2B352Homo sapiensMutation(s): 0 
Gene Names: RP2
UniProt & NIH Common Fund Data Resources
Find proteins for O75695 (Homo sapiens)
Explore O75695 
Go to UniProtKB:  O75695
PHAROS:  O75695
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ALF
Query on ALF

Download Ideal Coordinates CCD File 
D [auth A]TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.698α = 90
b = 77.943β = 90
c = 97.918γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-03-05
    Changes: Database references