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- PDB-9sqy: Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Compo... -

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Basic information

Entry
Database: PDB / ID: 9sqy
TitleCryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Composite map)
Components
  • (BRCA1-A complex subunit ...) x 2
  • (BRISC and BRCA1-A complex member ...) x 2
  • Lys-63-specific deubiquitinase BRCC36
  • Ubiquitin
KeywordsHYDROLASE / Deubiquitylating enzymes / JAMM/MPN family / ubiquitin chains / DNA damage repair
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 / ubiquitin-modified histone reader activity / mitotic G2/M transition checkpoint / tumor necrosis factor receptor binding ...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 / ubiquitin-modified histone reader activity / mitotic G2/M transition checkpoint / tumor necrosis factor receptor binding / hematopoietic stem cell proliferation / regulation of DNA damage checkpoint / K63-linked polyubiquitin modification-dependent protein binding / 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
Similarity search - Function
BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / BRISC and BRCA1-A complex member 1 / 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 ...BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / BRISC and BRCA1-A complex member 1 / 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 / 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: 2.92 Å
AuthorsFoglizzo, M. / Zeqiraj, E.
Funding support United Kingdom, 4items
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, U.M. / Ganji, R.S. / Wildsmith, G. / Chandler, F. / Campbell, L.J. / Calabrese, A.N. / Greenberg, R.A. / Zeqiraj, E.
History
DepositionSep 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 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

Downloads & links

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Assembly

Deposited unit
D: BRCA1-A complex subunit Abraxas 1
E: BRISC and BRCA1-A complex member 2
F: BRISC and BRCA1-A complex member 2
G: BRISC and BRCA1-A complex member 1
H: BRISC and BRCA1-A complex member 1
I: BRCA1-A complex subunit RAP80
J: BRCA1-A complex subunit RAP80
K: Ubiquitin
L: Ubiquitin
M: Ubiquitin
N: Ubiquitin
O: Ubiquitin
P: Ubiquitin
C: BRCA1-A complex subunit Abraxas 1
A: Lys-63-specific deubiquitinase BRCC36
B: Lys-63-specific deubiquitinase BRCC36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,08418
Polymers545,95416
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 DCIJ

#1: Protein BRCA1-A complex subunit Abraxas 1 / Coiled-coil domain-containing protein 98 / Protein FAM175A


Mass: 50623.969 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
#4: 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: 80243.945 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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BRISC and BRCA1-A complex member ... , 2 types, 4 molecules EFGH

#2: 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: 43721.602 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
#3: 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: 36594.930 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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Protein , 2 types, 8 molecules KLMNOPAB

#5: Protein
Ubiquitin / Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#6: 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: 36061.883 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

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Non-polymers , 1 types, 2 molecules

#7: 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 modificationN

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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

ComponentName: ARISC(E33A)-RAP80 in complex with K63-linked ubiquitin chains
Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 0.207 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
41Escherichia coli (E. coli)562
Buffer solutionpH: 7.3
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHEPES1
2150 mMSodium chlorideNaCl1
31 mMTris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Freshly purified ARISC(E33A)-RAP80 (at 0.6 mg/mL) was mixed with 1.5-fold molar excess of K63-linked heptaUb (Ub7) chains, and incubated in the presence of 0.025% (v/v) glutaraldehyde (Sigma- ...Details: Freshly purified ARISC(E33A)-RAP80 (at 0.6 mg/mL) was mixed with 1.5-fold molar excess of K63-linked heptaUb (Ub7) chains, and incubated in the presence of 0.025% (v/v) glutaraldehyde (Sigma-Aldrich) at room temperature for 4 min. The cross-linking reaction was then quenched by the addition of 100 mM Tris-HCl pH 7.5 prior to cryo-EM grids preparation.
Specimen supportDetails: UltraAuFoil 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).
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: blot force = 1 N; blot time = 6 s; waiting time = 27 s

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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: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.4 sec. / Electron dose: 45.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10649
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV / Phase plate: VOLTA PHASE PLATE

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Processing

EM software
IDNameVersionCategory
1crYOLOv1.6.1particle selection
4cryoSPARCv4.5.3CTF correction
7UCSF ChimeraXv1.6.1model fitting
9PHENIX1.21.1_5286:model refinement
10cryoSPARCv4.5.3initial Euler assignment
11cryoSPARCv4.5.3final Euler assignment
12cryoSPARCv4.5.3classification
13cryoSPARCv4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 789840
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214650 / Num. of class averages: 1 / Symmetry type: POINT

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