4KSK

Gumby/Fam105B in complex with ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein FAM105B
A, B
300Homo sapiensMutation(s): 1 
Gene Names: OTULIN (FAM105B)
EC: 3.4.19.12
Find proteins for Q96BN8 (Homo sapiens)
Go to Gene View: OTULIN
Go to UniProtKB:  Q96BN8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
C, D
80Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.273α = 90.00
b = 43.309β = 108.28
c = 113.918γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data scaling
HKL-3000data collection
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references
  • Version 1.2: 2013-07-03
    Type: Database references
  • Version 1.3: 2014-11-12
    Type: Structure summary