+Open data
-Basic information
Entry | Database: PDB / ID: 6gvw | ||||||
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Title | Crystal structure of the BRCA1-A complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Deubiquitinase complex / DUB / Lysine-63 linkage specific / BRCC36-containing / BRCA1A binding | ||||||
Function / homology | Function and homology information mitotic G2 DNA damage checkpoint signaling => GO:0007095 / : / : / BRISC complex / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs / BRCA1-A complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...mitotic G2 DNA damage checkpoint signaling => GO:0007095 / : / : / BRISC complex / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs / BRCA1-A complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / ubiquitin-modified histone reader activity / attachment of spindle microtubules to kinetochore / nuclear ubiquitin ligase complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / mitotic G2/M transition checkpoint / tumor necrosis factor receptor binding / protein K63-linked deubiquitination / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / hematopoietic stem cell proliferation / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / polyubiquitin modification-dependent protein binding / response to X-ray / mitotic spindle assembly / regulation of DNA repair / enzyme regulator activity / ubiquitin ligase complex / nuclear retinoid X receptor binding / positive regulation of DNA repair / spindle pole / metallopeptidase activity / double-strand break repair / site of double-strand break / chromatin organization / histone binding / microtubule binding / cysteine-type deubiquitinase activity / nuclear body / cell cycle / cell division / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / negative regulation of apoptotic process / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.75 Å | ||||||
Authors | Bunker, R.D. / Rabl, J. / Thoma, N.H. | ||||||
Citation | Journal: Mol Cell / Year: 2019 Title: Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation. Authors: Julius Rabl / Richard D Bunker / Andreas D Schenk / Simone Cavadini / Mark E Gill / Wassim Abdulrahman / Amparo Andrés-Pons / Martijn S Luijsterburg / Adel F M Ibrahim / Emma Branigan / ...Authors: Julius Rabl / Richard D Bunker / Andreas D Schenk / Simone Cavadini / Mark E Gill / Wassim Abdulrahman / Amparo Andrés-Pons / Martijn S Luijsterburg / Adel F M Ibrahim / Emma Branigan / Jacob D Aguirre / Aimee H Marceau / Claire Guérillon / Tewis Bouwmeester / Ulrich Hassiepen / Antoine H F M Peters / Martin Renatus / Laurent Gelman / Seth M Rubin / Niels Mailand / Haico van Attikum / Ronald T Hay / Nicolas H Thomä / Abstract: In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. ...In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. The BRCA1-A and BRISC complexes serve in DNA double-strand break repair and immune signaling and contain the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively. The molecular basis underlying BRCA1-A and BRISC function is currently unknown. Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2α, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains. Our work explains modularity in the BRCC36 DUB family, with different adaptor subunits conferring diversified targeting and regulatory functions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gvw.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gvw.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 6gvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/6gvw ftp://data.pdbj.org/pub/pdb/validation_reports/gv/6gvw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-BRCA1-A complex subunit ... , 2 types, 4 molecules AFEJ
#1: Protein | Mass: 46431.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abraxas1, Abra1, Ccdc98, Fam175a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8BPZ8 #5: Protein | Mass: 7327.536 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uimc1, Rap80, Rip110, Rxrip110 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5U5Q9 |
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-Protein , 1 types, 2 molecules BG
#2: Protein | Mass: 33711.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brcc3, Brcc36, C6.1a / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P46737, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases |
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-BRISC and BRCA1-A complex member ... , 2 types, 4 molecules CHDI
#3: Protein | Mass: 43915.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Babam2, Bre / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8K3W0 #4: Protein | Mass: 37155.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Babam1, Merit40, Nba1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q3UI43 |
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-Non-polymers , 2 types, 4 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.71 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 100 mM MES-KOH pH 5.6, 200 mM MgCl2, 8% (w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.75→30 Å / Num. obs: 53796 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 51.9 % / Biso Wilson estimate: 163 Å2 / CC1/2: 0.952 / Rmerge(I) obs: 0.173 / Rrim(I) all: 0.175 / Χ2: 1.19 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 3.75→3.814 Å / Redundancy: 52.8 % / Rmerge(I) obs: 15.709 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2661 / CC1/2: 0.476 / Rrim(I) all: 15.86 / Χ2: 1.45 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 3.75→29.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 131.227 / SU ML: 0.765 / Cross valid method: THROUGHOUT / ESU R Free: 0.728 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 209.67 Å2
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Refinement step | Cycle: LAST / Resolution: 3.75→29.99 Å
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Refine LS restraints |
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