8BVL

Crystal structure of the IBR-RING2 domain of HOIL-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for ubiquitylation by HOIL-1.

Wu, Q.Koliopoulos, M.G.Rittinger, K.Stieglitz, B.

(2022) Front Mol Biosci 9: 1098144-1098144

  • DOI: https://doi.org/10.3389/fmolb.2022.1098144
  • Primary Citation of Related Structures:  
    8BVL

  • PubMed Abstract: 

    The linear ubiquitin chain assembly complex synthesises linear Ub chains which constitute a binding and activation platform for components of the TNF signalling pathway. One of the components of LUBAC is the ubiquitin ligase HOIL-1 which has been shown to generate oxyester linkages on several proteins and on linear polysaccharides. We show that HOIL-1 activity requires linear tetra-Ub binding which enables HOIL-1 to mono-ubiquitylate linear Ub chains and polysaccharides. Furthermore, we describe the crystal structure of a C-terminal tandem domain construct of HOIL-1 comprising the IBR and RING2 domains. Interestingly, the structure reveals a unique bi-nuclear Zn-cluster which substitutes the second zinc finger of the canonical RING2 fold. We identify the C-terminal histidine of this bi-nuclear Zn-cluster as the catalytic base required for the ubiquitylation activity of HOIL-1. Our study suggests that the unique zinc-coordinating architecture of RING2 provides a binding platform for ubiquitylation targets.


  • Organizational Affiliation

    Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RanBP-type and C3HC4-type zinc finger-containing protein 1
A, B
145Homo sapiensMutation(s): 0 
Gene Names: RBCK1C20orf18RNF54UBCE7IP3XAP3XAP4
EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYM8 (Homo sapiens)
Explore Q9BYM8 
Go to UniProtKB:  Q9BYM8
PHAROS:  Q9BYM8
GTEx:  ENSG00000125826 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYM8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.908α = 90
b = 59.263β = 90.31
c = 57.206γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
ARP/wARPmodel building
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomCC2075

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection