4P0A

Crystal structure of HOIP PUB domain in complex with p97 PIM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of OTULIN to the PUB domain of HOIP controls NF-kappa B signaling.

Schaeffer, V.Akutsu, M.Olma, M.H.Gomes, L.C.Kawasaki, M.Dikic, I.

(2014) Mol Cell 54: 349-361

  • DOI: 10.1016/j.molcel.2014.03.016
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Linear ubiquitin chains are implicated in the regulation of the NF-κB pathway, immunity, and inflammation. They are synthesized by the LUBAC complex containing the catalytic subunit HOIL-1-interacting protein (HOIP) and are disassembled by the linear ...

    Linear ubiquitin chains are implicated in the regulation of the NF-κB pathway, immunity, and inflammation. They are synthesized by the LUBAC complex containing the catalytic subunit HOIL-1-interacting protein (HOIP) and are disassembled by the linear ubiquitin-specific deubiquitinase OTULIN. Little is known about the regulation of these opposing activities. Here we demonstrate that HOIP and OTULIN interact and act as a bimolecular editing pair for linear ubiquitin signals in vivo. The HOIP PUB domain binds to the PUB interacting motif (PIM) of OTULIN and the chaperone VCP/p97. Structural studies revealed the basis of high-affinity interaction with the OTULIN PIM. The conserved Tyr56 of OTULIN makes critical contacts with the HOIP PUB domain, and its phosphorylation negatively regulates this interaction. Functionally, HOIP binding to OTULIN is required for the recruitment of OTULIN to the TNF receptor complex and to counteract HOIP-dependent activation of the NF-κB pathway.


    Organizational Affiliation

    Institute of Biochemistry II, Goethe University Faculty of Medicine, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany. Electronic address: Ivan.Dikic@biochem2.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF31
A, C
184Homo sapiensMutation(s): 0 
Gene Names: RNF31ZIBRA
EC: 6.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
Find proteins for Q96EP0 (Homo sapiens)
Go to UniProtKB:  Q96EP0
NIH Common Fund Data Resources
PHAROS  Q96EP0
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transitional endoplasmic reticulum ATPase
B, D
10Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Go to UniProtKB:  P55072
NIH Common Fund Data Resources
PHAROS  P55072
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.04α = 90
b = 48.04β = 90
c = 266.622γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy