- EMDB-55056: BRCA1-A complex bound to K63-polyUbATA - closed form State C* -
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Open data
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Basic information
Entry
Database: EMDB / ID: EMD-55056
Title
BRCA1-A complex bound to K63-polyUbATA - closed form State C*
Map data
BRCA1-A complex bound to polyUbATA - closed form State C*
Sample
Complex: BRCA1-A complex bound to Lys-63 linked polyubiquitin chains
Complex: BRCA1-A complex
Protein or peptide: ABRAXAS (BRCA1-A complex subunit Abraxas 1)
Protein or peptide: BRCC36 (Lys-63-specific deubiquitinase BRCC36)
Protein or peptide: BRE (BRISC and BRCA1-A complex member 2)
Protein or peptide: BABAM1 (BRISC and BRCA1-A complex member 1)
Protein or peptide: RAP80 (BRCA1-A complex subunit RAP80)
Complex: Lys-63 Polyubiquitin chain analog
Protein or peptide: Ubiquitin
Protein or peptide: Ubiquitin
Keywords
Deubiquitinase / 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
Supramolecule #3: Lys-63 Polyubiquitin chain analog
Supramolecule
Name: Lys-63 Polyubiquitin chain analog / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7 Details: Visible ubiquitin moieties deriving from two copies of an uncleavable synthetic analog of Lys-63 polyubiquitin chains;
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.
Grid
Model: 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
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time: 5 s Blot Force: 0.
Details
3.3 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
Microscope
TFS KRIOS
Image recording
Film 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 beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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