5LJN

Structure of the HOIP PUB domain bound to SPATA2 PIM peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

SPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling.

Elliott, P.R.Leske, D.Hrdinka, M.Bagola, K.Fiil, B.K.McLaughlin, S.H.Wagstaff, J.Volkmar, N.Christianson, J.C.Kessler, B.M.Freund, S.M.Komander, D.Gyrd-Hansen, M.

(2016) Mol.Cell 63: 990-1005

  • DOI: 10.1016/j.molcel.2016.08.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The linear ubiquitin chain assembly complex (LUBAC) regulates immune signaling, and its function is regulated by the deubiquitinases OTULIN and CYLD, which associate with the catalytic subunit HOIP. However, the mechanism through which CYLD interacts ...

    The linear ubiquitin chain assembly complex (LUBAC) regulates immune signaling, and its function is regulated by the deubiquitinases OTULIN and CYLD, which associate with the catalytic subunit HOIP. However, the mechanism through which CYLD interacts with HOIP is unclear. We here show that CYLD interacts with HOIP via spermatogenesis-associated protein 2 (SPATA2). SPATA2 interacts with CYLD through its non-canonical PUB domain, which binds the catalytic CYLD USP domain in a CYLD B-box-dependent manner. Significantly, SPATA2 binding activates CYLD-mediated hydrolysis of ubiquitin chains. SPATA2 also harbors a conserved PUB-interacting motif that selectively docks into the HOIP PUB domain. In cells, SPATA2 is recruited to the TNF receptor 1 signaling complex and is required for CYLD recruitment. Loss of SPATA2 increases ubiquitination of LUBAC substrates and results in enhanced NOD2 signaling. Our data reveal SPATA2 as a high-affinity binding partner of CYLD and HOIP, and a regulatory component of LUBAC-mediated NF-κB signaling.


    Organizational Affiliation

    Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF31
A, B
173Homo sapiensMutation(s): 0 
Gene Names: RNF31 (ZIBRA)
EC: 2.3.2.31
Find proteins for Q96EP0 (Homo sapiens)
Go to Gene View: RNF31
Go to UniProtKB:  Q96EP0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Spermatogenesis-associated protein 2
C, D
8Homo sapiensMutation(s): 0 
Gene Names: SPATA2 (KIAA0757, PD1)
Find proteins for Q9UM82 (Homo sapiens)
Go to Gene View: SPATA2
Go to UniProtKB:  Q9UM82
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.233 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 89.040α = 90.00
b = 89.040β = 90.00
c = 53.563γ = 90.00
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2016-09-28
    Type: Database references