2Y8E

Crystal structure of D. melanogaster Rab6 GTPase bound to GMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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This is version 1.1 of the entry. See complete history


Literature

Structure of the Drosophila Melanogaster Rab6 Gtpase at 1.4 A Resolution

Walden, M.Jenkins, H.T.Edwards, T.A.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 744

  • DOI: 10.1107/S1744309111017453
  • Primary Citation of Related Structures:  
    2Y8E

  • PubMed Abstract: 
  • Rab6 is a small GTPase that belongs to the p21 Ras superfamily. It is involved in vesicle trafficking between the Golgi apparatus and endosomes/ER in eukaryotes. The GDP-bound inactive protein undergoes conformational changes when the nucleotide is exchanged to GTP, allowing Rab6 to interact with a variety of different effector proteins ...

    Rab6 is a small GTPase that belongs to the p21 Ras superfamily. It is involved in vesicle trafficking between the Golgi apparatus and endosomes/ER in eukaryotes. The GDP-bound inactive protein undergoes conformational changes when the nucleotide is exchanged to GTP, allowing Rab6 to interact with a variety of different effector proteins. To further understand how these changes affect downstream protein binding, the crystal structure of Rab6 from Drosophila melanogaster has been solved to 1.4 Å resolution, the highest resolution for a Rab6 structure to date. The crystals belonged to space group C2, with unit-cell parameters a=116.5, b=42.71, c=86.86 Å, α=90, β=133.12, γ=90°. The model was refined to an R factor of 14.5% and an Rfree of 17.3%.


    Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAB-PROTEIN 6A, B179Drosophila melanogasterMutation(s): 0 
Gene Names: Rab6wrtCG6601
UniProt
Find proteins for O18334 (Drosophila melanogaster)
Explore O18334 
Go to UniProtKB:  O18334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18334
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B],
G [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.52α = 90
b = 42.71β = 133.12
c = 86.86γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Database references, Version format compliance