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- EMDB-55118: Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map) -

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Basic information

Entry
Database: EMDB / ID: EMD-55118
TitleCryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)
Map dataCryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)
Sample
  • Complex: ARISCdC(E33A) in complex with K63-linked ubiquitin chains
    • Protein or peptide: Ubiquitin
    • 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
  • Ligand: ZINC ION
KeywordsDeubiquitylating enzymes / JAMM/MPN family / ubiquitin chains / DNA damage repair / HYDROLASE
Function / homology
Function and homology information


peroxisome signal sequence receptor activity / nuclear ubiquitin ligase complex / BRISC complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / response to vitamin B6 / BRCA1-A complex / attachment of spindle microtubules to kinetochore / mitotic G2/M transition checkpoint / tumor necrosis factor receptor binding / regulation of DNA damage checkpoint ...peroxisome signal sequence receptor activity / nuclear ubiquitin ligase complex / BRISC complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / response to vitamin B6 / BRCA1-A complex / attachment of spindle microtubules to kinetochore / mitotic G2/M transition checkpoint / tumor necrosis factor receptor binding / regulation of DNA damage checkpoint / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / response to ionizing radiation / K63-linked deubiquitinase activity / mitotic G2 DNA damage checkpoint signaling / positive regulation of NLRP3 inflammasome complex assembly / mitotic spindle assembly / DNA repair-dependent chromatin remodeling / response to X-ray / protein deubiquitination / polyubiquitin modification-dependent protein binding / 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 / regulation of DNA repair / 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 / NRIF signals cell death from the nucleus / Regulation of PTEN localization / positive regulation of DNA repair / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / cellular response to ionizing radiation / 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 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI / Downregulation of TGF-beta receptor signaling / 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 / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Negative regulation of FGFR3 signaling / Nonhomologous End-Joining (NHEJ) / Ubiquitin-dependent degradation of Cyclin D / Fanconi Anemia Pathway / Deactivation of the beta-catenin transactivating complex / Peroxisomal protein import / SCF-beta-TrCP mediated degradation of Emi1
Similarity search - Function
FAM175 family, BRCA1-A complex, Abraxas 1 subunit / 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 / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease ...FAM175 family, BRCA1-A complex, Abraxas 1 subunit / 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 / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / : / 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 / BRISC and BRCA1-A complex member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsFoglizzo M / Degtjarik O / Zeqiraj E
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Z51522X/1 United Kingdom
Wellcome Trust222531/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/T029471/1 United Kingdom
Wellcome Trust221524/Z/20/Z United Kingdom
CitationJournal: To Be Published
Title: Mechanism of K63-linked polyubiquitin recognition and cleavage by the BRCA1-A complex
Authors: Foglizzo M / Datta A / Degtjarik O / Perera H / Liburd J / Sykora UM / Ganji RS / Wildsmith G / Chandler F / Campbell LJ / Calabrese AN / Greenberg RA / Zeqiraj E
History
DepositionSep 23, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55118.png

Downloads & links

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Map

FileDownload / File: emd_55118.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0572
Minimum - Maximum-0.0018139448 - 2.2661145
Average (Standard dev.)0.0010809193 (±0.02411846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ARISCdC(E33A) in complex with K63-linked ubiquitin chains

EntireName: ARISCdC(E33A) in complex with K63-linked ubiquitin chains
Components
  • Complex: ARISCdC(E33A) in complex with K63-linked ubiquitin chains
    • Protein or peptide: Ubiquitin
    • 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
  • Ligand: ZINC ION

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Supramolecule #1: ARISCdC(E33A) in complex with K63-linked ubiquitin chains

SupramoleculeName: ARISCdC(E33A) in complex with K63-linked ubiquitin chains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 131 KDa

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Macromolecule #1: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

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Macromolecule #2: BRCA1-A complex subunit Abraxas 1

MacromoleculeName: BRCA1-A complex subunit Abraxas 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.013449 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKL EVLFQGTMEG ESTSAVLSGF VLGALAFQHL NTDSDTEGFL LGEVKGEAKN SITDSQMDD VEVVYTIDIQ KYIPCYQLFS FYNSSGEVNE QALKKILSNV KKNVVGWYKF RRHSDQIMTF RERLLHKNLQ E HFSNQDLV ...String:
MWSHPQFEKG GGSGGGSGGS AWSHPQFEKL EVLFQGTMEG ESTSAVLSGF VLGALAFQHL NTDSDTEGFL LGEVKGEAKN SITDSQMDD VEVVYTIDIQ KYIPCYQLFS FYNSSGEVNE QALKKILSNV KKNVVGWYKF RRHSDQIMTF RERLLHKNLQ E HFSNQDLV FLLLTPSIIT ESCSTHRLEH SLYKPQKGLF HRVPLVVANL GMSEQLGYKT VSGSCMSTGF SRAVQTHSSK FF EEDGSLK EVHKINEMYA SLQEELKSIC KKVEDSEQAV DKLVKDVNRL KREIEKRRGA QIQAA

UniProtKB: BRCA1-A complex subunit Abraxas 1

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Macromolecule #3: Lys-63-specific deubiquitinase BRCC36

MacromoleculeName: Lys-63-specific deubiquitinase BRCC36 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.061883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAVQVVQAVQ AVHLESDAFL VCLNHALSTE KEAVMGLCIG ELNDDTRSDS KFAYTGTEMR TVAEKVDAVR IVHIHSVIIL RRSDKRKDR VEISPEQLSA ASTEAERLAE LTGRPMRVVG WYHSHPHITV WPSHVDVRTQ AMYQMMDQGF VGLIFSCFIE D KNTKTGRV ...String:
MAVQVVQAVQ AVHLESDAFL VCLNHALSTE KEAVMGLCIG 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 #4: BRISC and BRCA1-A complex member 2

MacromoleculeName: BRISC and BRCA1-A complex member 2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.721602 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAMSPEVALN RISPMLSPFI SSVVRNGKVG LDATNCLRIT DLKSGCTSLT PGPNCDRFKL HIPYAGETLK WDIIFNAQYP ELPPDFIFG EDAEFLPDPS ALQNLASWNP SNPECLLLVV KELVQQYHQF QCSRLRESSR LMFEYQTLLE EPQYGENMEI Y AGKKNNWT ...String:
GAMSPEVALN RISPMLSPFI SSVVRNGKVG LDATNCLRIT DLKSGCTSLT PGPNCDRFKL HIPYAGETLK WDIIFNAQYP ELPPDFIFG EDAEFLPDPS ALQNLASWNP SNPECLLLVV KELVQQYHQF QCSRLRESSR LMFEYQTLLE EPQYGENMEI Y AGKKNNWT GEFSARFLLK LPVDFSNIPT YLLKDVNEDP GEDVALLSVS FEDTEATQVY PKLYLSPRIE HALGGSSALH IP AFPGGGC LIDYVPQVCH LLTNKVQYVI QGYHKRREYI AAFLSHFGTG VVEYDAEGFT KLTLLLMWKD FCFLVHIDLP LFF PRDQPT LTFQSVYHFT NSGQLYSQAQ KNYPYSPRWD GNEMAKRAKA YFKTFVPQFQ EAAFANGKL

UniProtKB: BRISC and BRCA1-A complex member 2

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.8 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
25.0 mMHEPES4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid
150.0 mMNaClsodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 3.8e-07 kPa
Details: UltrAuFoil R1.2/1.3 300-mesh grids (Quantifoil Micro Tools GmbH) were glow-discharged for 1 min at 12 mA and 0.38 mBar pressure using a PELCO easiGlow system (Ted Pella).
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blot force = 1 N; blot time = 6 s; waiting time = 27 s.
DetailsFreshly purified ARISCdC(E33A) (at 0.8 mg/mL) was mixed with 1.5-fold molar excess of K63-linked tetraUb (Ub4) chains, and incubated in the presence of 0.025% (v/v) glutaraldehyde (Sigma-Aldrich) at room temperature for 4 min. Cross-linking reactions were then quenched by the addition of 100 mM Tris-HCl pH 7.5 prior to cryo-EM grids preparation.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 58037 / Average exposure time: 3.4 sec. / Average electron dose: 45.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 165000
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: 2194750
CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: A previously determined 3D volume was used as the startup model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 54452
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final 3D classificationNumber classes: 3

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX (ver. v1.6.1)
Output model

PDB-9sqv:
Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)

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