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- PDB-9so9: BRCA1-A complex bound to K63-oligoUbATA - closed form StateC* -

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Basic information

Entry
Database: PDB / ID: 9so9
TitleBRCA1-A complex bound to K63-oligoUbATA - closed form StateC*
Components
  • (BRCA1-A complex subunit ...) x 2
  • (BRISC and BRCA1-A complex member ...) x 2
  • (Polyubiquitin- ...) x 2
  • Lys-63-specific deubiquitinase BRCC36
  • Ubiquitin
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 / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / positive regulation of DNA repair / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to ionizing radiation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / NOTCH3 Activation and Transmission of Signal to the Nucleus / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Asymmetric localization of PCP proteins / Nonhomologous End-Joining (NHEJ) / Fanconi Anemia Pathway / Ubiquitin-dependent degradation of Cyclin D / Negative regulation of FGFR3 signaling / Peroxisomal protein import
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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / 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: 3.4 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 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 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
I: BRISC and BRCA1-A complex member 1
J: BRCA1-A complex subunit RAP80
L: Ubiquitin
M: Polyubiquitin-C
N: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,69215
Polymers394,56113
Non-polymers1312
Water00
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
Source: (gene. exp.) Homo sapiens (human) / Gene: UIMC1, RAP80, RXRIP110 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96RL1

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Protein , 2 types, 3 molecules BGL

#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
#6: Protein Ubiquitin / Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG48

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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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Polyubiquitin- ... , 2 types, 2 molecules MN

#7: Protein Polyubiquitin-C


Mass: 8547.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG48
#8: Protein Polyubiquitin-C


Mass: 8636.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG48

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Non-polymers , 1 types, 2 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
1BRCA1-A complex bound to Lys-63 linked polyubiquitin chainsCOMPLEX#1-#50RECOMBINANT
2BRCA1-A complexCOMPLEX#1-#51RECOMBINANT
3Lys-63 Polyubiquitin chain analogCOMPLEX#6-#71RECOMBINANTVisible ubiquitin moieties deriving from two copies of an uncleavable synthetic analog of Lys-63 polyubiquitin chains;
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.454 MDaNO
210.369 MDaNO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
43Spodoptera frugiperda (fall armyworm)7108
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 probe chains (concentration > 10 uM - see paper), and incubated at 37C for 15 minutes; Octyl glucoside was added at 10X concentration prior to freezing.
Specimen supportDetails: 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: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1250 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: 2.28 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11785
Details: 8017 images collected without tilt, 5 shots / hole at rim of hole (no particles at center due to lensing); 3768 images tilted 30 degrees, collected from same grid, different session, same ...Details: 8017 images collected without tilt, 5 shots / hole at rim of hole (no particles at center due to lensing); 3768 images tilted 30 degrees, collected from same grid, different session, same imaging conditions, 4 shots / hole. Tilted and straight combined directly in data processing.

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2Topaz0.2.5aparticle selection
3crYOLO1.9.9particle selection
4EPUimage acquisition
6cryoSPARC4CTF correction
9UCSF ChimeraX1.9model fitting
10Coot0.9.8model fitting
12Servalcatmodel refinement
13PHENIX1.21model refinement
14cryoSPARC4initial Euler assignment
15cryoSPARC4final Euler assignment
16cryoSPARC4classification
17cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74906 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetails (eV)Initial refinement model-ID
16gvw

6gvw

6gvwmutated back to human1
21ubq

1ubq

1ubq2
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00921500
ELECTRON MICROSCOPYf_angle_d1.11629093
ELECTRON MICROSCOPYf_dihedral_angle_d13.8828065
ELECTRON MICROSCOPYf_chiral_restr0.0593239
ELECTRON MICROSCOPYf_plane_restr0.0153751

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