3CWZ

Structure of RAB6(GTP)-R6IP1 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

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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
  • Primary Citation of Related Structures:  
    3CWZ

  • 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 angstroms resolution ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-6AA188Homo sapiensMutation(s): 1 
Gene Names: RAB6A, RAB6
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P20340 (Homo sapiens)
Explore P20340 
Go to UniProtKB:  P20340
PHAROS:  P20340
GTEx:  ENSG00000175582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20340
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rab6-interacting protein 1B384Mus musculusMutation(s): 0 
Gene Names: Rab6ip1, Dennd5a
Membrane Entity: Yes 
UniProt
Find proteins for Q6PAL8 (Mus musculus)
Explore Q6PAL8 
Go to UniProtKB:  Q6PAL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PAL8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
D [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 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: 3.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.24α = 90
b = 100.24β = 90
c = 299.25γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2016-12-14
    Changes: Structure summary
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations