6KC5

HOIP-HOIPIN1 complex

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-06-27 Released: 2020-04-15 
  • Deposition Author(s): Sato, Y., Fukai, S.
  • Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses.

Oikawa, D.Sato, Y.Ohtake, F.Komakura, K.Hanada, K.Sugawara, K.Terawaki, S.Mizukami, Y.Phuong, H.T.Iio, K.Obika, S.Fukushi, M.Irie, T.Tsuruta, D.Sakamoto, S.Tanaka, K.Saeki, Y.Fukai, S.Tokunaga, F.

(2020) Commun Biol 3: 163-163

  • DOI: https://doi.org/10.1038/s42003-020-0882-8
  • Primary Citation of Related Structures:  
    6KC5, 6KC6

  • PubMed Abstract: 

    The NF-κB and interferon antiviral signaling pathways play pivotal roles in inflammatory and innate immune responses. The LUBAC ubiquitin ligase complex, composed of the HOIP, HOIL-1L, and SHARPIN subunits, activates the canonical NF-κB pathway through Met1-linked linear ubiquitination. We identified small-molecule chemical inhibitors of LUBAC, HOIPIN-1 and HOIPIN-8. Here we show that HOIPINs down-regulate not only the proinflammatory cytokine-induced canonical NF-κB pathway, but also various pathogen-associated molecular pattern-induced antiviral pathways. Structural analyses indicated that HOIPINs inhibit the RING-HECT-hybrid reaction in HOIP by modifying the active Cys885, and residues in the C-terminal LDD domain, such as Arg935 and Asp936, facilitate the binding of HOIPINs to LUBAC. HOIPINs effectively induce cell death in activated B cell-like diffuse large B cell lymphoma cells, and alleviate imiquimod-induced psoriasis in model mice. These results reveal the molecular and cellular bases of LUBAC inhibition by HOIPINs, and demonstrate their potential therapeutic uses.


  • Organizational Affiliation

    Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF31A [auth B]225Homo sapiensMutation(s): 0 
Gene Names: RNF31ZIBRA
EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EP0 (Homo sapiens)
Explore Q96EP0 
Go to UniProtKB:  Q96EP0
PHAROS:  Q96EP0
GTEx:  ENSG00000092098 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EP0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D5U (Subject of Investigation/LOI)
Query on D5U

Download Ideal Coordinates CCD File 
F [auth B]2-[3-(2-methoxyphenyl)-3-oxidanylidene-propyl]benzoic acid
C17 H16 O4
BGYZYPMQNIMFRN-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
K [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B],
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B,
C [auth B],
D [auth B],
E [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.35α = 90
b = 60.227β = 90
c = 92.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16H06575
Japan Society for the Promotion of ScienceJapan18H02619
Japan Society for the Promotion of ScienceJapan18H05501
Japan Society for the Promotion of ScienceJapan18K06967
Japan Society for the Promotion of ScienceJapan19H05296

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary