4LJO

Structure of an active ligase (HOIP)/ubiquitin transfer complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.564 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP.

Stieglitz, B.Rana, R.R.Koliopoulos, M.G.Morris-Davies, A.C.Schaeffer, V.Christodoulou, E.Howell, S.Brown, N.R.Dikic, I.Rittinger, K.

(2013) Nature 503: 422-426

  • DOI: 10.1038/nature12638
  • Primary Citation of Related Structures:  4LJP, 4LJQ

  • PubMed Abstract: 
  • Linear ubiquitin chains are important regulators of cellular signalling pathways that control innate immunity and inflammation through nuclear factor (NF)-κB activation and protection against tumour necrosis factor-α-induced apoptosis. They are synth ...

    Linear ubiquitin chains are important regulators of cellular signalling pathways that control innate immunity and inflammation through nuclear factor (NF)-κB activation and protection against tumour necrosis factor-α-induced apoptosis. They are synthesized by HOIP, which belongs to the RBR (RING-between-RING) family of E3 ligases and is the catalytic component of LUBAC (linear ubiquitin chain assembly complex), a multisubunit E3 ligase. RBR family members act as RING/HECT hybrids, employing RING1 to recognize ubiquitin-loaded E2 while a conserved cysteine in RING2 subsequently forms a thioester intermediate with the transferred or 'donor' ubiquitin. Here we report the crystal structure of the catalytic core of HOIP in its apo form and in complex with ubiquitin. The carboxy-terminal portion of HOIP adopts a novel fold that, together with a zinc-finger, forms a ubiquitin-binding platform that orients the acceptor ubiquitin and positions its α-amino group for nucleophilic attack on the E3∼ubiquitin thioester. The C-terminal tail of a second ubiquitin molecule is located in close proximity to the catalytic cysteine, providing a unique snapshot of the ubiquitin transfer complex containing both donor and acceptor ubiquitin. These interactions are required for activation of the NF-κB pathway in vivo, and they explain the determinants of linear ubiquitin chain specificity by LUBAC.


    Organizational Affiliation

    Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF31
A
223Homo sapiensGene Names: RNF31 (ZIBRA)
EC: 6.3.2.-
Find proteins for Q96EP0 (Homo sapiens)
Go to Gene View: RNF31
Go to UniProtKB:  Q96EP0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
B
76Bos taurusGene Names: UBA52 (UBCEP2)
Find proteins for P63048 (Bos taurus)
Go to Gene View: UBA52
Go to UniProtKB:  P63048
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.564 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 45.950α = 90.00
b = 45.950β = 90.00
c = 133.010γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
CCP4refinement
PDB_EXTRACTdata extraction
CCP4data scaling
XSCALEdata scaling
REFMACrefinement
CCP4data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references
  • Version 1.2: 2013-12-18
    Type: Database references
  • Version 1.3: 2014-10-08
    Type: Structure summary
  • Version 1.4: 2017-11-15
    Type: Refinement description