3CWZ

Structure of RAB6(GTP)-R6IP1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for recruitment of Rab6-interacting protein 1 to Golgi via a RUN domain.

Recacha, R.Boulet, A.Jollivet, F.Monier, S.Houdusse, A.Goud, B.Khan, A.R.

(2009) Structure 17: 21-30

  • DOI: 10.1016/j.str.2008.10.014

  • PubMed Abstract: 
  • Small GTPase Rab6 regulates vesicle trafficking at the level of Golgi via recruitment of numerous and unrelated effectors. The crystal structure of Rab6a(GTP) in complex with a 378-residue internal fragment of the effector Rab6IP1 was solved at 3.2 a ...

    Small GTPase Rab6 regulates vesicle trafficking at the level of Golgi via recruitment of numerous and unrelated effectors. The crystal structure of Rab6a(GTP) in complex with a 378-residue internal fragment of the effector Rab6IP1 was solved at 3.2 angstroms resolution. This Rab6IP1 region encompasses an all alpha-helical RUN domain followed in tandem by a PLAT domain that adopts a beta sandwich fold. The structure reveals that the first and last alpha helices of the RUN domain mediate binding to switch I, switch II, and the interswitch region of Rab6. It represents the largest Rab-effector complex determined to date. Comparisons with the recent structure of Rab6 in complex with an unrelated effector, human golgin GCC185, reveals significant conformational changes in the conserved hydrophobic triad of Rab6. Flexibility in the switch and interswitch regions of Rab6 mediates recognition of compositionally distinct alpha-helical coiled coils, thereby contributing to Rab6 promiscuity in effector recruitment.


    Organizational Affiliation

    School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-6A
A
188Homo sapiensMutation(s): 1 
Gene Names: RAB6A (RAB6)
Find proteins for P20340 (Homo sapiens)
Go to Gene View: RAB6A
Go to UniProtKB:  P20340
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rab6-interacting protein 1
B
384Mus musculusMutation(s): 0 
Gene Names: Dennd5a (Rab6ip1)
Find proteins for Q6PAL8 (Mus musculus)
Go to UniProtKB:  Q6PAL8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.246 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 100.240α = 90.00
b = 100.240β = 90.00
c = 299.250γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2016-12-14
    Type: Structure summary