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- EMDB-55054: Structure of BRCA1-A complex bound to oligoUbATA - open form -

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Basic information

Entry
Database: EMDB / ID: EMD-55054
TitleStructure of BRCA1-A complex bound to oligoUbATA - open form
Map data
Sample
  • Complex: BRCA1-A complex bound to Lys-63 linked polyubiquitin chains
    • Complex: BRCA1-A complex
      • Protein or peptide: BRCA1-A complex subunit Abraxas 1
      • Protein or peptide: Lys-63-specific deubiquitinase BRCC36
      • Protein or peptide: BRISC and BRCA1-A complex member 1
      • Protein or peptide: BRISC and BRCA1-A complex member 2
      • Protein or peptide: BRCA1-A complex subunit RAP80
    • Complex: Lys-63 Polyubiquitin chain analog
      • Protein or peptide: Ubiquitin
KeywordsDeubiquitinase / DNA repair / Metalloprotein / Ubiquitin chains / METAL BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMurachelli AG / Sixma TK
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Oncode Institute Netherlands
CitationJournal: Biorxiv / Year: 2026
Title: A ubiquitin chain-feeding mechanism for BRCA1-A
Authors: Murachelli AG / El Oualid F / Sixma TK
History
DepositionSep 12, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55054.png

Downloads & links

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Map

FileDownload / File: emd_55054.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1362 Å
Density
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.098979995 - 0.28263244
Average (Standard dev.)-0.00013662003 (±0.0043711686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 436.30078 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55054_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: deepEMhancer-sharpened

Fileemd_55054_additional_1.map
AnnotationdeepEMhancer-sharpened
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_55054_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55054_half_map_2.map
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Sample components

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Entire : BRCA1-A complex bound to Lys-63 linked polyubiquitin chains

EntireName: BRCA1-A complex bound to Lys-63 linked polyubiquitin chains
Components
  • Complex: BRCA1-A complex bound to Lys-63 linked polyubiquitin chains
    • Complex: BRCA1-A complex
      • Protein or peptide: BRCA1-A complex subunit Abraxas 1
      • Protein or peptide: Lys-63-specific deubiquitinase BRCC36
      • Protein or peptide: BRISC and BRCA1-A complex member 1
      • Protein or peptide: BRISC and BRCA1-A complex member 2
      • Protein or peptide: BRCA1-A complex subunit RAP80
    • Complex: Lys-63 Polyubiquitin chain analog
      • Protein or peptide: Ubiquitin

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Supramolecule #1: BRCA1-A complex bound to Lys-63 linked polyubiquitin chains

SupramoleculeName: BRCA1-A complex bound to Lys-63 linked polyubiquitin chains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 369 KDa

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Supramolecule #2: BRCA1-A complex

SupramoleculeName: BRCA1-A complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Lys-63 Polyubiquitin chain analog

SupramoleculeName: Lys-63 Polyubiquitin chain analog / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Details: Visible ubiquitin moieties deriving from two copies of an uncleavable synthetic analog of Lys-63 polyubiquitin chains;
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BRCA1-A complex subunit Abraxas 1

MacromoleculeName: BRCA1-A complex subunit Abraxas 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEGESTSAVL SGFVLGALAF QHLNTDSDTE GFLLGEVKGE AKNSITDSQM DDVEVVYTID IQKYIPCYQL FSFYNSSGEV NEQALKKILS NVKKNVVGWY KFRRHSDQIM TFRERLLHKN LQEHFSNQDL VFLLLTPSII TESCSTHRLE HSLYKPQKGL FHRVPLVVAN ...String:
MEGESTSAVL SGFVLGALAF QHLNTDSDTE GFLLGEVKGE AKNSITDSQM DDVEVVYTID IQKYIPCYQL FSFYNSSGEV NEQALKKILS NVKKNVVGWY KFRRHSDQIM TFRERLLHKN LQEHFSNQDL VFLLLTPSII TESCSTHRLE HSLYKPQKGL FHRVPLVVAN LGMSEQLGYK TVSGSCMSTG FSRAVQTHSS KFFEEDGSLK EVHKINEMYA SLQEELKSIC KKVEDSEQAV DKLVKDVNRL KREIEKRRGA QIQAAREKNI QKDPQENIFL CQALRTFFPN SEFLHSCVMS LKNRHVSKSS CNYNHHLDVV DNLTLMVEHT DIPEASPAST PQIIKHKALD LDDRWQFKRS RLLDTQDKRS KADTGSSNQD KASKMSSPET DEEIEKMKGF GEYSRSPTF

UniProtKB: BRCA1-A complex subunit Abraxas 1

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Macromolecule #2: Lys-63-specific deubiquitinase BRCC36

MacromoleculeName: Lys-63-specific deubiquitinase BRCC36 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAVQVVQAVQ AVHLESDAFL VCLNHALSTE KEEVMGLCIG ELNDDTRSDS KFAYTGTEMR TVAEKVDAVR IVHIHSVIIL RRSDKRKDRV EISPEQLSAA STEAERLAEL TGRPMRVVGW YHSHPHITVW PSHVDVRTQA MYQMMDQGFV GLIFSCFIED KNTKTGRVLY ...String:
MAVQVVQAVQ AVHLESDAFL VCLNHALSTE KEEVMGLCIG ELNDDTRSDS KFAYTGTEMR TVAEKVDAVR IVHIHSVIIL RRSDKRKDRV EISPEQLSAA STEAERLAEL TGRPMRVVGW YHSHPHITVW PSHVDVRTQA MYQMMDQGFV GLIFSCFIED KNTKTGRVLY TCFQSIQAQK SSESLHGPRD FWSSSQHISI EGQKEEERYE RIEIPIHIVP HVTIGKVCLE SAVELPKILC QEEQDAYRRI HSLTHLDSVT KIHNGSVFTK NLCSQMSAVS GPLLQWLEDR LEQNQQHLQE LQQEKEELMQ ELSSLE

UniProtKB: Lys-63-specific deubiquitinase BRCC36

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Macromolecule #3: BRISC and BRCA1-A complex member 1

MacromoleculeName: BRISC and BRCA1-A complex member 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSPEVALNRI SPMLSPFISS VVRNGKVGLD ATNCLRITDL KSGCTSLTPG PNCDRFKLHI PYAGETLKWD IIFNAQYPEL PPDFIFGED AEFLPDPSAL QNLASWNPSN PECLLLVVKE LVQQYHQFQC SRLRESSRLM FEYQTLLEEP QYGENMEIYA G KKNNWTGE ...String:
MSPEVALNRI SPMLSPFISS VVRNGKVGLD ATNCLRITDL KSGCTSLTPG PNCDRFKLHI PYAGETLKWD IIFNAQYPEL PPDFIFGED AEFLPDPSAL QNLASWNPSN PECLLLVVKE LVQQYHQFQC SRLRESSRLM FEYQTLLEEP QYGENMEIYA G KKNNWTGE FSARFLLKLP VDFSNIPTYL LKDVNEDPGE DVALLSVSFE DTEATQVYPK LYLSPRIEHA LGGSSALHIP AF PGGGCLI DYVPQVCHLL TNKVQYVIQG YHKRREYIAA FLSHFGTGVV EYDAEGFTKL TLLLMWKDFC FLVHIDLPLF FPR DQPTLT FQSVYHFTNS GQLYSQAQKN YPYSPRWDGN EMAKRAKAYF KTFVPQFQEA AFANGKL

UniProtKB: BRISC and BRCA1-A complex member 1

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Macromolecule #4: BRISC and BRCA1-A complex member 2

MacromoleculeName: BRISC and BRCA1-A complex member 2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHSA ALEVLFQGPG MEVAEPSSPT EEEEEEEEHS AEPRPRTRSN PEGAEDRAVG AQASVGSRSE GEGEAASADD GSLNTSGAG PKSWQVPPPA PEVQIRTPRV NCPEKVIICL DLSEEMSLPK LESFNGSKTN ALNVSQKMIE MFVRTKHKID K SHEFALVV ...String:
MAHHHHHHSA ALEVLFQGPG MEVAEPSSPT EEEEEEEEHS AEPRPRTRSN PEGAEDRAVG AQASVGSRSE GEGEAASADD GSLNTSGAG PKSWQVPPPA PEVQIRTPRV NCPEKVIICL DLSEEMSLPK LESFNGSKTN ALNVSQKMIE MFVRTKHKID K SHEFALVV VNDDTAWLSG LTSDPRELCS CLYDLETASC STFNLEGLFS LIQQKTELPV TENVQTIPPP YVVRTILVYS RP PCQPQFS LTEPMKKMFQ CPYFFFDVVY IHNGTEEKEE EMSWKDMFAF MGSLDTKGTS YKYEVALAGP ALELHNCMAK LLA HPLQRP CQSHASYSLL EEEDEAIEVE ATV

UniProtKB: BRISC and BRCA1-A complex member 2

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Macromolecule #5: BRCA1-A complex subunit RAP80

MacromoleculeName: BRCA1-A complex subunit RAP80 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASWSHPQFE KGALEVLFQG PGKGLQDTGG TVNYFWGIPF CPDGVDPNQY TKVILCQLEV YQKSLKMAQR QLLNKKGFGE PVLPRPPSL IQNECGQGEQ ASEKNECISE DMGDEDKEER QESRASDWHS KTKDFQESSI KSLKEKLLLE EEPTTSHGQS S QGIVEETS EEG

UniProtKB: BRCA1-A complex subunit RAP80

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Macromolecule #6: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQ(DRG)ESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.33 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMC8H18N2O4S2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid (HEPES)
0.05 %C14H28O6Octyl beta-D-glucopyranoside (Octyl glucoside)
2.0 mMC9H15O6Ptris(2-carboxyethyl)phosphine (TCEP)

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.
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time: 5 s Blot Force: 0.
Details3.3 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.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11785 / Average exposure time: 2.28 sec. / Average electron dose: 50.0 e/Å2
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.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Model was created ab-initio from picked particles
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Details: Open vs closed form classification / Number images used: 416938
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

1ubq

source_name: PDB, initial_model_type: experimental model

6gvw

source_name: PDB, initial_model_type: experimental modelmutated back to human
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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