9SQV | pdb_00009sqv

Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9SQV

This is version 1.1 of the entry. See complete history

Literature

Mechanism of K63-linked polyubiquitin recognition and cleavage by the BRCA1-A complex.

Foglizzo, M.Datta, A.Degtjarik, O.Perera, H.Liburd, J.Sykora, U.M.Ganji, S.R.Wildsmith, G.Chandler, F.Campbell, L.J.Calabrese, A.N.Greenberg, R.A.Zeqiraj, E.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-75795-y
  • Primary Citation Related Structures: 
    9SQV, 9SQW, 9SQY

  • PubMed Abstract: 

    Deubiquitylases modulate cellular processes by removing monoubiquitin or cleaving polyubiquitin chains. The ARISC-RAP80 complex partners with BRCA1-BARD1 to form the BRCA1-A supercomplex, which recognises K63-linked ubiquitin chains at DNA damage sites. ARISC-RAP80 contains multiple ubiquitin-binding sites, yet how these influence recognition and cleavage of K63-polyubiquitylated substrates remains unknown. We discover that a composite three-subunit interface allows ARISC-RAP80 to position K63-linked polyubiquitin chains in its catalytic site. Substrate recognition is further supported by RAP80 and non-catalytic ubiquitin-binding sites that impose a compact conformation on K63-polyubiquitylated substrates. This mechanism exploits the inherent flexibility of long ubiquitin chains and differs considerably from other deubiquitylases. Structure-guided mutageneses validate ubiquitin chain interactions, and cell-based assays demonstrate a functional role of the observed interfaces in chromatin recruitment. Our findings define mechanisms of polyubiquitin chain decoding and cleavage by ARISC-RAP80, linking ubiquitin reading and erasing functions to BRCA1-A mediated DNA damage responses.


  • Organizational Affiliation
    • Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK. m.foglizzo@leeds.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 244.88 kDa 
  • Atom Count: 12,545 
  • Modeled Residue Count: 1,572 
  • Deposited Residue Count: 2,158 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UbiquitinA [auth G],
B [auth H]
76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
BRCA1-A complex subunit Abraxas 1
C, D
302Homo sapiensMutation(s): 0 
Gene Names: ABRAXAS1ABRA1CCDC98FAM175AUNQ496/PRO1013
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UWZ7 (Homo sapiens)
Explore Q6UWZ7 
Go to UniProtKB:  Q6UWZ7
GTEx:  ENSG00000163322 
Entity Groups
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UniProt GroupQ6UWZ7
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Lys-63-specific deubiquitinase BRCC36E [auth A],
F [auth B]
316Homo sapiensMutation(s): 1 
Gene Names: BRCC3BRCC36C6.1ACXorf53
EC: 3.4.19
UniProt & NIH Common Fund Data Resources
Find proteins for P46736 (Homo sapiens)
Explore P46736 
Go to UniProtKB:  P46736
GTEx:  ENSG00000185515 
Entity Groups
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UniProt GroupP46736
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
BRISC and BRCA1-A complex member 2G [auth F],
H [auth E]
385Homo sapiensMutation(s): 0 
Gene Names: BABAM2BRCC45BRE
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXR7 (Homo sapiens)
Explore Q9NXR7 
Go to UniProtKB:  Q9NXR7
GTEx:  ENSG00000158019 
Entity Groups
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UniProt GroupQ9NXR7
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4.5.3
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/Z51522X/1
Wellcome TrustUnited Kingdom222531/Z/21/Z
Medical Research Council (MRC, United Kingdom)United KingdomMR/T029471/1
Wellcome TrustUnited Kingdom221524/Z/20/Z

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-05
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Data collection, Database references