4DBG

Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative

• PDB DOI: https://doi.org/10.2210/pdb4DBG/pdb

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


• Deposited: 2012-01-15 Released: 2012-04-04 
• Deposition Author(s): Yagi, H., Hiromoto, T., Mizushima, T., Kurimoto, E., Kato, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.253 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex

Yagi, H., Ishimoto, K., Hiromoto, T., Fujita, H., Mizushima, T., Uekusa, Y., Yagi-Utsumi, M., Kurimoto, E., Noda, M., Uchiyama, S., Tokunaga, F., Iwai, K., Kato, K.

(2012) EMBO Rep 13: 462-468

• PubMed: 22430200 
• DOI: https://doi.org/10.1038/embor.2012.24
• Primary Citation of Related Structures:  
  4DBG


• PubMed Abstract: 
  

  HOIL-1L and its binding partner HOIP are essential components of the E3-ligase complex that generates linear ubiquitin (Ub) chains, which are critical regulators of NF-κB activation. Using crystallographic and mutational approaches, we characterize the unexpected structural basis for the specific interaction between the Ub-like domain (UBL) of HOIL-1L and the Ub-associated domain (UBA) of HOIP. Our data indicate the functional significance of this non-canonical mode of UBA-UBL interaction in E3 complex formation and subsequent NF-κB activation. This study highlights the versatility and specificity of protein-protein interactions involving Ub/UBLs and their cognate proteins.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.23 kDa 
• Atom Count: 1,859 
• Modelled Residue Count: 228 
• Deposited Residue Count: 267 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RanBP-type and C3HC4-type zinc finger-containing protein 1	A	105	Homo sapiens	Mutation(s): 0  Gene Names: RBCK1 EC: 6.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYM8 (Homo sapiens) Explore Q9BYM8  Go to UniProtKB:  Q9BYM8
PHAROS:  Q9BYM8 GTEx:  ENSG00000125826

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RING finger protein 31	B	162	Homo sapiens	Mutation(s): 0  Gene Names: RNF31 EC: 6.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EP0 (Homo sapiens) Explore Q96EP0  Go to UniProtKB:  Q96EP0
PHAROS:  Q96EP0 GTEx:  ENSG00000092098

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.253 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.973	α = 90
b = 64.973	β = 90
c = 161.291	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Yagi, H., Hiromoto, T., Mizushima, T., Kurimoto, E., Kato, K.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Structure summary
• Version 1.2: 2012-05-16
  Changes: Database references
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Structure summary