9SMP | pdb_00009smp

BRCA1-A complex bound to K63-polyUbATA - open form double State P

PDB DOI: https://doi.org/10.2210/pdb9SMP/pdb
EM Map EMD-55039: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2025-09-08 Released: 2026-06-17
Deposition Author(s): Murachelli, A.G., Sixma, T.K.
Funding Organization(s): Oncode Institute, Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A ubiquitin chain-feeding mechanism for BRCA1-A.

Murachelli, A.G., El Oualid, F., Sixma, T.K.

(2026) Nat Commun 17

PubMed: 42581048 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-75797-w
Primary Citation Related Structures:
9SMN, 9SMP, 9SMR, 9SMS, 9SNA, 9SO9

PubMed Abstract:
The BRCA1-A complex is a multi-subunit, metallo-deubiquitinating enzyme (metallo-DUB) involved in genome maintenance. BRCA1-A displays strict specificity for K63-linked ubiquitin, with a strong preference for long chains, but the mechanistic basis for this selectivity has remained unclear. To address this, we have developed an activity-based probe that is specific for metallo-DUBs and mimics di- or polyubiquitin chains of any linkage (di- and poly-ubiquitin _ATA). We have solved cryoEM structures of BRCA1-A bound to K63-linked probe chains of various length, capturing multiple conformational and catalytic states. The structures reveal how allosteric regulation of catalysis occurs within the complex and how BRCA1-A uses auxiliary ubiquitin-binding sites to engage substrate by avidity and to trigger processive cleavage. Crucially, avidity and processivity can only apply to long polyubiquitin chains, explaining BRCA1-A's substrate preference. Together, these results establish BRCA1-A as a chain-shortening DUB specialised for trimming extended K63-linked polyubiquitin chains.

Organizational Affiliation

Netherlands Cancer Institute and Oncode Institute, Amsterdam, the Netherlands. a.murachelli@nki.nl.

Macromolecule Content

Total Structure Weight: 437.61 kDa
Atom Count: 24,573
Modeled Residue Count: 3,071
Deposited Residue Count: 3,864
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BRCA1-A complex subunit Abraxas 1	A, F	409	Homo sapiens	Mutation(s): 0 Gene Names: ABRAXAS1, ABRA1, CCDC98, FAM175A, UNQ496/PRO1013
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UWZ7 (Homo sapiens) Explore Q6UWZ7 Go to UniProtKB: Q6UWZ7
GTEx: ENSG00000163322
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6UWZ7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lys-63-specific deubiquitinase BRCC36	B, G	316	Homo sapiens	Mutation(s): 0 Gene Names: BRCC3, BRCC36, C6.1A, CXorf53 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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46736
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BRISC and BRCA1-A complex member 2	C, H	383	Homo sapiens	Mutation(s): 0 Gene Names: BABAM2, BRCC45, BRE
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXR7 (Homo sapiens) Explore Q9NXR7 Go to UniProtKB: Q9NXR7
GTEx: ENSG00000158019
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NXR7
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BRISC and BRCA1-A complex member 1	D, I	349	Homo sapiens	Mutation(s): 0 Gene Names: BABAM1, C19orf62, MERIT40, NBA1, HSPC142
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWV8 (Homo sapiens) Explore Q9NWV8 Go to UniProtKB: Q9NWV8
GTEx: ENSG00000105393
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NWV8
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BRCA1-A complex subunit RAP80	E, J	171	Homo sapiens	Mutation(s): 0 Gene Names: UIMC1, RAP80, RXRIP110
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RL1 (Homo sapiens) Explore Q96RL1 Go to UniProtKB: Q96RL1
GTEx: ENSG00000087206
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96RL1
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	K, M	76	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG48
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	L	76	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	N	76	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	O [auth S], P [auth T], Q [auth U], R [auth V]	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth G] SDF format, chain S [auth B] MOL2 format, chain T [auth G] MOL2 format, chain S [auth B] mmCIF format, chain T [auth G] mmCIF format, chain S [auth B]	S [auth B], T [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Focus chain T [auth G] Interactions & Density Focus chain S [auth B] Focus chain T [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAB Query on DAB	K, M	L-PEPTIDE LINKING	C₄ H₁₀ N₂ O₂		ALA
A1JPL Query on A1JPL	L	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		--
A1JPT Query on A1JPT	N	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		--