6F6P

Crystal structure of tetrameric human Rabin8 GEF domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of tetrameric human Rabin8 GEF domain.

Vetter, M.Boegholm, N.Christensen, A.Bhogaraju, S.Andersen, M.B.Lorentzen, A.Lorentzen, E.

(2018) Proteins 86: 405-413

  • DOI: https://doi.org/10.1002/prot.25455
  • Primary Citation of Related Structures:  
    6F6P

  • PubMed Abstract: 

    Rab GTPases and their effectors, activators and guanine nucleotide exchange factors (GEFs) are essential for vesicular transport. Rab8 and its GEF Rabin8 function in formation of the cilium organelle important for developmental signaling and sensory reception. Here, we show by size exclusion chromatography and analytical ultracentrifugation that Rabin8 exists in equilibrium between dimers and tetramers. The crystal structure of tetrameric Rabin8 GEF domain reveals an occluded Rab8 binding site suggesting that this oligomer is enzymatically inactive, a notion we verify experimentally using Rabin8/Rab8 GEF assays. We outline a procedure for the purification of active dimeric Rabin8 GEF-domain for in vitro activity assays.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, D-82152, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rab-3A-interacting protein
A, B, D
106Homo sapiensMutation(s): 0 
Gene Names: RAB3IPRABIN8
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QF0 (Homo sapiens)
Explore Q96QF0 
Go to UniProtKB:  Q96QF0
PHAROS:  Q96QF0
GTEx:  ENSG00000127328 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QF0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rab-3A-interacting protein106Homo sapiensMutation(s): 0 
Gene Names: RAB3IPRABIN8
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QF0 (Homo sapiens)
Explore Q96QF0 
Go to UniProtKB:  Q96QF0
PHAROS:  Q96QF0
GTEx:  ENSG00000127328 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QF0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.322α = 90
b = 77β = 90
c = 137.258γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NNFDenmarkNNF15OC0014164

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2018-03-14
    Changes: Database references