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- EMDB-55041: BRCA1-A complex: Ubiquitin bound to BRE at the wrist site (focuse... -

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Basic information

Entry
Database: EMDB / ID: EMD-55041
TitleBRCA1-A complex: Ubiquitin bound to BRE at the wrist site (focused 3D class)
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: 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
    • 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 / 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 ...peroxisome signal sequence receptor activity / BRISC complex / 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 / response to ionizing radiation / hematopoietic stem cell proliferation / mitotic G2 DNA damage checkpoint signaling / DNA repair-dependent chromatin remodeling / mitotic spindle assembly / polyubiquitin modification-dependent protein binding / regulation of DNA repair / 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 / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Stabilization of p53 / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling
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) / FAM175 family / BRCA1-A complex subunit Abraxas 1 MPN domain / Ubiquitin-interacting motif. ...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) / 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. / 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 / 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: 3.3 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) 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_55041.png

Downloads & links

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Map

FileDownload / File: emd_55041.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.092 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.31587005 - 0.9184924
Average (Standard dev.)-0.00024566194 (±0.017817352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 419.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55041_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_55041_additional_1.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55041_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55041_half_map_2.map
Projections & Slices
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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: 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
    • 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-#4
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: #5
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 / Number of copies: 1 / 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: BRISC and BRCA1-A complex member 2

MacromoleculeName: BRISC and BRCA1-A complex member 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: BRISC and BRCA1-A complex member 1

MacromoleculeName: BRISC and BRCA1-A complex member 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: BRCA1-A complex subunit RAP80

MacromoleculeName: BRCA1-A complex subunit RAP80 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / 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 #5: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV 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 % (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: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa / Details: 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 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 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Details: Classification on the wrist ubiquitin / Number images used: 114857
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: 123929 / Software - Name: cryoSPARC (ver. 4)
Details: Focused classification on active site configuration. This is only one state in the ensemble - see paper for details
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

b0lm


Chain - Chain ID: s / Chain - Source name: ModelArchive / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9sms:
BRCA1-A complex: Ubiquitin bound to BRE at the wrist site (focused 3D class)

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