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Yorodumi- PDB-7cmz: Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cmz | |||||||||||||||
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Title | Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8 | |||||||||||||||
Components |
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Keywords | PROTEIN BINDING/HYDROLASE / TOPBP1 / PROTEIN BINDING-HYDROLASE complex | |||||||||||||||
Function / homology | Function and homology information broken chromosome clustering / histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / BRCA1-B complex / negative regulation of rDNA heterochromatin formation / phosphorylation-dependent protein binding ...broken chromosome clustering / histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / BRCA1-B complex / negative regulation of rDNA heterochromatin formation / phosphorylation-dependent protein binding / chromatin-protein adaptor activity / homologous recombination / histone H3K36 demethylase activity / DNA replication checkpoint signaling / 2-oxoglutarate-dependent dioxygenase activity / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / mitotic DNA replication checkpoint signaling / DNA metabolic process / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / double-strand break repair via alternative nonhomologous end joining / positive regulation of transcription by RNA polymerase I / mitotic G2 DNA damage checkpoint signaling / histone H3K9 demethylase activity / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / condensed nuclear chromosome / DNA replication initiation / histone demethylase activity / chromosome organization / male germ cell nucleus / transcription coregulator activity / methylated histone binding / protein serine/threonine kinase activator activity / Condensation of Prophase Chromosomes / DNA damage checkpoint signaling / HDMs demethylate histones / G2/M DNA damage checkpoint / double-strand break repair via homologous recombination / brain development / G1/S transition of mitotic cell cycle / PML body / spindle pole / chromosome / actin cytoskeleton / Processing of DNA double-strand break ends / site of double-strand break / nuclear membrane / Regulation of TP53 Activity through Phosphorylation / nuclear body / iron ion binding / DNA repair / chromatin binding / centrosome / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å | |||||||||||||||
Authors | Che, S.Y. / Ma, S. / Cao, C. / Yao, Z. / Shi, L. / Yang, N. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Sci Adv / Year: 2021 Title: PHF8-promoted TOPBP1 demethylation drives ATR activation and preserves genome stability. Authors: Ma, S. / Cao, C. / Che, S. / Wang, Y. / Su, D. / Liu, S. / Gong, W. / Liu, L. / Sun, J. / Zhao, J. / Wang, Q. / Song, N. / Ge, T. / Guo, Q. / Tian, S. / Chen, C.D. / Zhang, T. / Wang, J. / ...Authors: Ma, S. / Cao, C. / Che, S. / Wang, Y. / Su, D. / Liu, S. / Gong, W. / Liu, L. / Sun, J. / Zhao, J. / Wang, Q. / Song, N. / Ge, T. / Guo, Q. / Tian, S. / Chen, C.D. / Zhang, T. / Wang, J. / Ding, X. / Yang, F. / Ying, G. / Yang, J. / Zhang, K. / Zhu, Y. / Yao, Z. / Yang, N. / Shi, L. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cmz.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cmz.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 7cmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cmz_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 7cmz_full_validation.pdf.gz | 426.7 KB | Display | |
Data in XML | 7cmz_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 7cmz_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/7cmz ftp://data.pdbj.org/pub/pdb/validation_reports/cm/7cmz | HTTPS FTP |
-Related structure data
Related structure data | 3al2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26059.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOPBP1, KIAA0259 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92547 |
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#2: Protein/peptide | Mass: 2422.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q9UPP1, [histone H3]-dimethyl-L-lysine36 demethylase, [histone H3]-dimethyl-L-lysine9 demethylase |
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 35.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion Details: Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 31, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.695→40 Å / Num. obs: 24740 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Χ2: 0.958 / Net I/σ(I): 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3al2 Resolution: 1.695→34.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.231 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.52 Å2 / Biso mean: 14.848 Å2 / Biso min: 4.59 Å2
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Refinement step | Cycle: final / Resolution: 1.695→34.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.695→1.739 Å / Rfactor Rfree error: 0
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