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- EMDB-55040: Structure of apo BRCA1-A complex in presence of K63-oligoUbATA -

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Basic information

Entry
Database: EMDB / ID: EMD-55040
TitleStructure of apo BRCA1-A complex in presence of K63-oligoUbATA
Map dataApo-BRCA1-A complex
Sample
  • Complex: BRCA1-A complex without substrate in the active sites
    • 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 2
    • Protein or peptide: BRISC and BRCA1-A complex member 1
    • Protein or peptide: BRCA1-A complex subunit RAP80
  • Ligand: ZINC ION
  • Ligand: water
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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsMurachelli AG / Sixma TK
Funding support Netherlands, 2 items
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 AG / El Oualid F / Sixma TK
History
DepositionSep 9, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55040.png

Downloads & links

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Map

FileReleased
AnnotationApo-BRCA1-A complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 432 pix.
= 551.794 Å		1.28 Å/pix.
x 432 pix.
= 551.794 Å		1.28 Å/pix.
x 432 pix.
= 551.794 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.15822725 - 0.42076582
Average (Standard dev.)-0.000075066826 (±0.0046755136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 551.7936 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55040_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: deepEMhancer-sharpened map

Fileemd_55040_additional_1.map
AnnotationdeepEMhancer-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55040_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55040_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BRCA1-A complex without substrate in the active sites

EntireName: BRCA1-A complex without substrate in the active sites
Components
  • Complex: BRCA1-A complex without substrate in the active sites
    • 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 2
    • Protein or peptide: BRISC and BRCA1-A complex member 1
    • Protein or peptide: BRCA1-A complex subunit RAP80
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: BRCA1-A complex without substrate in the active sites

SupramoleculeName: BRCA1-A complex without substrate in the active sites / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: "Synthetic, non-cleavable Lys63-linked polyubiquitin chains were included in the sample, but the complex did not engage them."
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 454 KDa

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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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.731754 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEGESTSAVL SGFVLGALAF QHLNTDSDTE GFLLGEVKGE AKNSITDSQM DDVEVVYTID IQKYIPCYQL FSFYNSSGEV NEQALKKIL SNVKKNVVGW YKFRRHSDQI MTFRERLLHK NLQEHFSNQD LVFLLLTPSI ITESCSTHRL EHSLYKPQKG L FHRVPLVV ...String:
MEGESTSAVL SGFVLGALAF QHLNTDSDTE GFLLGEVKGE AKNSITDSQM DDVEVVYTID IQKYIPCYQL FSFYNSSGEV NEQALKKIL SNVKKNVVGW YKFRRHSDQI MTFRERLLHK NLQEHFSNQD LVFLLLTPSI ITESCSTHRL EHSLYKPQKG L FHRVPLVV ANLGMSEQLG YKTVSGSCMS TGFSRAVQTH SSKFFEEDGS LKEVHKINEM YASLQEELKS ICKKVEDSEQ AV DKLVKDV NRLKREIEKR RGAQIQAARE KNIQKDPQEN IFLCQALRTF FPNSEFLHSC VMSLKNRHVS KSSCNYNHHL DVV DNLTLM VEHTDIPEAS PASTPQIIKH KALDLDDRWQ FKRSRLLDTQ DKRSKADTGS SNQDKASKMS SPETDEEIEK MKGF GEYSR SPTF

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 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.119918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAVQVVQAVQ AVHLESDAFL VCLNHALSTE KEEVMGLCIG ELNDDTRSDS KFAYTGTEMR TVAEKVDAVR IVHIHSVIIL RRSDKRKDR VEISPEQLSA ASTEAERLAE LTGRPMRVVG WYHSHPHITV WPSHVDVRTQ AMYQMMDQGF VGLIFSCFIE D KNTKTGRV ...String:
MAVQVVQAVQ AVHLESDAFL VCLNHALSTE KEEVMGLCIG ELNDDTRSDS KFAYTGTEMR TVAEKVDAVR IVHIHSVIIL RRSDKRKDR VEISPEQLSA ASTEAERLAE LTGRPMRVVG WYHSHPHITV WPSHVDVRTQ AMYQMMDQGF VGLIFSCFIE D KNTKTGRV LYTCFQSIQA QKSSESLHGP RDFWSSSQHI SIEGQKEEER YERIEIPIHI VPHVTIGKVC LESAVELPKI LC QEEQDAY RRIHSLTHLD SVTKIHNGSV FTKNLCSQMS AVSGPLLQWL EDRLEQNQQH LQELQQEKEE LMQELSSLE

UniProtKB: Lys-63-specific deubiquitinase BRCC36

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Macromolecule #3: BRISC and BRCA1-A complex member 2

MacromoleculeName: BRISC and BRCA1-A complex member 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.593473 KDa
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 2

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Macromolecule #4: BRISC and BRCA1-A complex member 1

MacromoleculeName: BRISC and BRCA1-A complex member 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.796379 KDa
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 1

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Macromolecule #5: BRCA1-A complex subunit RAP80

MacromoleculeName: BRCA1-A complex subunit RAP80 / type: protein_or_peptide / ID: 5 / Details: StrepII tagged / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.15817 KDa
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: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 % (v/v)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 / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa / Details: Current: 30 mA
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 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.

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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: 4623 / Average exposure time: 3.88 sec. / Average electron dose: 50.0 e/Å2
Details: Four shots per hole, at quadrant positions (particle number was low in the centre owing to lensing effects)
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: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 647888 / Details: Clean particles.
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 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4)
Details: Maasked resolution. For unmasked resolution see FSC plot in this deposition.
Number images used: 279338
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 2 / Avg.num./class: 310000 / Software - Name: cryoSPARC (ver. 4)
Details: This deposition refers to the open state of the complex. There is a closed state in the ensemble, see related depositions.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9smn


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsStarting model was fitted with coot and refined with Phenix real space refine and Refmac Servalcat.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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