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- PDB-9smr: Structure of apo BRCA1-A complex in presence of K63-oligoUbATA -

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Basic information

Entry
Database: PDB / ID: 9smr
TitleStructure of apo BRCA1-A complex in presence of K63-oligoUbATA
Components
  • (BRCA1-A complex subunit ...) x 2
  • (BRISC and BRCA1-A complex member ...) x 2
  • Lys-63-specific deubiquitinase BRCC36
KeywordsMETAL BINDING PROTEIN / Deubiquitinase / DNA repair / Metalloprotein / Ubiquitin chains
Function / homology
Function and homology information


peroxisome signal sequence receptor activity / BRISC complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / BRCA1-A complex / attachment of spindle microtubules to kinetochore / ubiquitin-modified histone reader activity / nuclear ubiquitin ligase complex / mitotic G2/M transition checkpoint / regulation of DNA damage checkpoint / tumor necrosis factor receptor binding ...peroxisome signal sequence receptor activity / BRISC complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / BRCA1-A complex / attachment of spindle microtubules to kinetochore / ubiquitin-modified histone reader activity / nuclear ubiquitin ligase complex / mitotic G2/M transition checkpoint / regulation of DNA damage checkpoint / tumor necrosis factor receptor binding / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / metal-dependent deubiquitinase activity / K63-linked deubiquitinase activity / response to ionizing radiation / hematopoietic stem cell proliferation / mitotic G2 DNA damage checkpoint signaling / DNA repair-dependent chromatin remodeling / positive regulation of NLRP3 inflammasome complex assembly / mitotic spindle assembly / response to X-ray / protein deubiquitination / polyubiquitin modification-dependent protein binding / regulation of DNA repair / ubiquitin ligase complex / enzyme regulator activity / positive regulation of DNA repair / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Metalloprotease DUBs / spindle pole / metallopeptidase activity / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromatin organization / Processing of DNA double-strand break ends / histone binding / microtubule binding / cysteine-type deubiquitinase activity / nuclear body / cell division / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / negative regulation of apoptotic process / signal transduction / proteolysis / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
FAM175 family, BRCA1-A complex, Abraxas 1 subunit / BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / BRISC and BRCA1-A complex member 1 / BRCA1-A complex subunit BRE / Brain and reproductive organ-expressed protein (BRE) / Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain ...FAM175 family, BRCA1-A complex, Abraxas 1 subunit / BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / BRISC and BRCA1-A complex member 1 / BRCA1-A complex subunit BRE / Brain and reproductive organ-expressed protein (BRE) / Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain / FAM175 family / BRCA1-A complex subunit Abraxas 1 MPN domain / Ubiquitin-interacting motif. / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / : / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Lys-63-specific deubiquitinase BRCC36 / BRCA1-A complex subunit Abraxas 1 / BRCA1-A complex subunit RAP80 / BRISC and BRCA1-A complex member 1 / BRISC and BRCA1-A complex member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsMurachelli, A.G. / Sixma, T.K.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Oncode Institute Netherlands
Netherlands Organisation for Scientific Research (NWO)OCENW.M.21.288 Netherlands
CitationJournal: Biorxiv / Year: 2026
Title: A ubiquitin chain-feeding mechanism for BRCA1-A
Authors: Murachelli, A.G. / El Oualid, F. / Sixma, T.K.
History
DepositionSep 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRCA1-A complex subunit Abraxas 1
B: Lys-63-specific deubiquitinase BRCC36
C: BRISC and BRCA1-A complex member 2
D: BRISC and BRCA1-A complex member 1
E: BRCA1-A complex subunit RAP80
F: BRCA1-A complex subunit Abraxas 1
G: Lys-63-specific deubiquitinase BRCC36
H: BRISC and BRCA1-A complex member 2
J: BRCA1-A complex subunit RAP80
I: BRISC and BRCA1-A complex member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,93012
Polymers368,79910
Non-polymers1312
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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BRCA1-A complex subunit ... , 2 types, 4 molecules AFEJ

#1: Protein BRCA1-A complex subunit Abraxas 1 / Coiled-coil domain-containing protein 98 / Protein FAM175A


Mass: 46731.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABRAXAS1, ABRA1, CCDC98, FAM175A, UNQ496/PRO1013 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6UWZ7
#5: Protein BRCA1-A complex subunit RAP80 / Receptor-associated protein 80 / Retinoid X receptor-interacting protein 110 / Ubiquitin ...Receptor-associated protein 80 / Retinoid X receptor-interacting protein 110 / Ubiquitin interaction motif-containing protein 1


Mass: 19158.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: StrepII tagged / Source: (gene. exp.) Homo sapiens (human) / Gene: UIMC1, RAP80, RXRIP110 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96RL1

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Protein , 1 types, 2 molecules BG

#2: Protein Lys-63-specific deubiquitinase BRCC36 / BRCA1-A complex subunit BRCC36 / BRCA1/BRCA2-containing complex subunit 3 / BRCA1/BRCA2-containing ...BRCA1-A complex subunit BRCC36 / BRCA1/BRCA2-containing complex subunit 3 / BRCA1/BRCA2-containing complex subunit 36 / BRISC complex subunit BRCC36


Mass: 36119.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCC3, BRCC36, C6.1A, CXorf53 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P46736, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases

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BRISC and BRCA1-A complex member ... , 2 types, 4 molecules CHDI

#3: Protein BRISC and BRCA1-A complex member 2 / BRCA1-A complex subunit BRE / BRCA1/BRCA2-containing complex subunit 45 / Brain and reproductive ...BRCA1-A complex subunit BRE / BRCA1/BRCA2-containing complex subunit 45 / Brain and reproductive organ-expressed protein


Mass: 43593.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BABAM2, BRCC45, BRE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NXR7
#4: Protein BRISC and BRCA1-A complex member 1 / Mediator of RAP80 interactions and targeting subunit of 40 kDa / New component of the BRCA1-A complex


Mass: 38796.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BABAM1, C19orf62, MERIT40, NBA1, HSPC142 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NWV8

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BRCA1-A complex without substrate in the active sites / Type: COMPLEX
Details: "Synthetic, non-cleavable Lys63-linked polyubiquitin chains were included in the sample, but the complex did not engage them."
Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.454 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Details: 0.5% octyl-glucoside, 150 mM NaCl, 20 mM HEPES, pH 8.0 buffer was added as 10x to protein in 150 mM NaCl, 20 mM HEPES pH 8.0 prior to grid freezing.
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
220 mM2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid (HEPES)C8H18N2O4S1
30.05 % (v/v)Octyl beta-D-glucopyranoside (Octyl glucoside)C14H28O61
42 mMtris(2-carboxyethyl)phosphine (TCEP)C9H15O6P1
SpecimenConc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 3.3 mg/ml of BRCA1-A complex were mixed with 1 ul of uncleavable K63-linked ubiquitin chains (concentration > 10 uM - see paper), and incubated at 37C for 15 minutes; Octyl glucoside was ...Details: 3.3 mg/ml of BRCA1-A complex were mixed with 1 ul of uncleavable K63-linked ubiquitin chains (concentration > 10 uM - see paper), and incubated at 37C for 15 minutes; Octyl glucoside was added at 10X concentration prior to freezing. Bound ubiquitin is present at the wrist site, but not in either active site.
Specimen supportDetails: Current: 30 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot time: 5 s Blot Force: 0

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.88 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4623
Details: Four shots per hole, at quadrant positions (particle number was low in the centre owing to lensing effects)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2Topaz0.2.5aparticle selection
3crYOLO1.9.9particle selection
6cryoSPARC4CTF correction
9Coot0.9.8model fitting
11PHENIX1.21.2model refinement
12Servalcatmodel refinement
13cryoSPARC4initial Euler assignment
14cryoSPARC4final Euler assignment
15cryoSPARC4classification
16cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 647888 / Details: Clean particles.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279338
Details: Maasked resolution. For unmasked resolution see FSC plot in this deposition.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Starting model was fitted with coot and refined with Phenix real space refine and Refmac Servalcat.
Atomic model buildingPDB-ID: 9SMN

9smn


Accession code: 9SMN / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.25 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319973
ELECTRON MICROSCOPYf_angle_d0.66827039
ELECTRON MICROSCOPYf_dihedral_angle_d13.1657464
ELECTRON MICROSCOPYf_chiral_restr0.0422989
ELECTRON MICROSCOPYf_plane_restr0.013493

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