4KSL

Gumby/Fam105B in complex with linear di-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis.

Rivkin, E.Almeida, S.M.Ceccarelli, D.F.Juang, Y.C.MacLean, T.A.Srikumar, T.Huang, H.Dunham, W.H.Fukumura, R.Xie, G.Gondo, Y.Raught, B.Gingras, A.C.Sicheri, F.Cordes, S.P.

(2013) Nature 498: 318-324

  • DOI: 10.1038/nature12296
  • Primary Citation of Related Structures:  
    4KSL, 4KSJ, 4KSK

  • PubMed Abstract: 
  • A complex interaction of signalling events, including the Wnt pathway, regulates sprouting of blood vessels from pre-existing vasculature during angiogenesis. Here we show that two distinct mutations in the (uro)chordate-specific gumby (also called F ...

    A complex interaction of signalling events, including the Wnt pathway, regulates sprouting of blood vessels from pre-existing vasculature during angiogenesis. Here we show that two distinct mutations in the (uro)chordate-specific gumby (also called Fam105b) gene cause an embryonic angiogenic phenotype in gumby mice. Gumby interacts with disheveled 2 (DVL2), is expressed in canonical Wnt-responsive endothelial cells and encodes an ovarian tumour domain class of deubiquitinase that specifically cleaves linear ubiquitin linkages. A crystal structure of gumby in complex with linear diubiquitin reveals how the identified mutations adversely affect substrate binding and catalytic function in line with the severity of their angiogenic phenotypes. Gumby interacts with HOIP (also called RNF31), a key component of the linear ubiquitin assembly complex, and decreases linear ubiquitination and activation of NF-κB-dependent transcription. This work provides support for the biological importance of linear (de)ubiquitination in angiogenesis, craniofacial and neural development and in modulating Wnt signalling.


    Organizational Affiliation

    Samuel Lunenfeld Research Institute, Mt Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein FAM105BABEGIKMOQSUW276Homo sapiensMutation(s): 1 
Gene Names: FAM105BOTULIN
EC: 3.4.19.12
Find proteins for Q96BN8 (Homo sapiens)
Explore Q96BN8 
Go to UniProtKB:  Q96BN8
NIH Common Fund Data Resources
PHAROS  Q96BN8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CCDFHJLNPRTVX156Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.622α = 90
b = 186.087β = 90
c = 219.698γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Structure summary