7YUI | pdb_00007yui

Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights into the enzymatic activity of E3 ligase HOIL-1L and its regulation by the linear ubiquitin chain binding.

Xu, X.Wang, Y.Zhang, Y.Wang, Y.Yin, Y.Peng, C.Gong, X.Li, M.Zhang, Y.Zhang, M.Tang, Y.Zhou, X.Liu, H.Pan, L.

(2023) Sci Adv 9: eadi4599-eadi4599

  • DOI: https://doi.org/10.1126/sciadv.adi4599
  • Primary Citation of Related Structures:  
    7YUI, 7YUJ

  • PubMed Abstract: 

    Heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1L) serves as a unique E3 ligase to catalyze the mono-ubiquitination of relevant protein or sugar substrates and plays vital roles in numerous cellular processes in mammals. However, the molecular mechanism underpinning the E3 activity of HOIL-1L and the related regulatory mechanism remain elusive. Here, we report the crystal structure of the catalytic core region of HOIL-1L and unveil the key catalytic triad residues of HOIL-1L. Moreover, we discover that HOIL-1L contains two distinct linear di-ubiquitin binding sites that can synergistically bind to linear tetra-ubiquitin, and the binding of HOIL-1L with linear tetra-ubiquitin can promote its E3 activity. The determined HOIL-1L/linear tetra-ubiquitin complex structure not only elucidates the detailed binding mechanism of HOIL-1L with linear tetra-ubiquitin but also uncovers a unique allosteric ubiquitin-binding site for the activation of HOIL-1L. In all, our findings provide mechanistic insights into the E3 activity of HOIL-1L and its regulation by the linear ubiquitin chain binding.


  • Organizational Affiliation
    • School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-C308Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RanBP-type and C3HC4-type zinc finger-containing protein 1234Homo sapiensMutation(s): 0 
Gene Names: RBCK1
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.5α = 90
b = 90.304β = 90
c = 117.439γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21621002

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references, Structure summary
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary