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Yorodumi- PDB-3shv: Crystal structure of human MCPH1 tandem BRCT domains-gamma H2AX c... -
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-Basic information
Entry | Database: PDB / ID: 3shv | ||||||
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Title | Crystal structure of human MCPH1 tandem BRCT domains-gamma H2AX complex | ||||||
Components |
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Keywords | CELL CYCLE / tandem brct domains H2AX | ||||||
Function / homology | Function and homology information regulation of chromosome condensation / neuronal stem cell population maintenance / XY body / regulation of centrosome cycle / protein localization to centrosome / response to ionizing radiation / site of DNA damage / establishment of mitotic spindle orientation / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends ...regulation of chromosome condensation / neuronal stem cell population maintenance / XY body / regulation of centrosome cycle / protein localization to centrosome / response to ionizing radiation / site of DNA damage / establishment of mitotic spindle orientation / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of DNA repair / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / meiotic cell cycle / PRC2 methylates histones and DNA / DNA damage checkpoint signaling / condensed nuclear chromosome / male germ cell nucleus / Defective pyroptosis / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / cellular response to gamma radiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / bone development / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / cerebral cortex development / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / double-strand break repair / nucleosome / cellular senescence / mitotic cell cycle / site of double-strand break / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / histone binding / regulation of inflammatory response / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / damaged DNA binding / nuclear speck / Amyloid fiber formation / protein heterodimerization activity / centrosome / DNA damage response / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Shao, Z.H. / Li, F.D. / Yan, W. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Specific recognition of phosphorylated tail of H2AX by the tandem BRCT domains of MCPH1 revealed by complex structure Authors: Shao, Z.H. / Li, F.D. / Sy, S.M.-H. / Yan, W. / Zhang, Z. / Gong, D. / Wen, B. / Huen, M.S.Y. / Gong, Q. / Wu, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3shv.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3shv.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3shv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/3shv ftp://data.pdbj.org/pub/pdb/validation_reports/sh/3shv | HTTPS FTP |
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-Related structure data
Related structure data | 3shtSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22872.615 Da / Num. of mol.: 2 / Fragment: residues 639-835 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEM0 #2: Protein/peptide | Mass: 1235.236 Da / Num. of mol.: 2 / Fragment: residues in UNP 134-143 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104 #3: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE IS FROM GENBANK NP_078872.2 MICROCEPHALIN ISOFORM 1. MICROCEPHALIN HAS A NATURAL ...THIS SEQUENCE IS FROM GENBANK NP_078872.2 MICROCEPHA | |
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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: 2.67 Å3/Da / Density % sol: 53.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Sodium acetate trihydrate, 100mM TRIS hydrochloride(pH 8.5), 30%(w/v) PEG4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: plane grating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. all: 31233 / Num. obs: 31077 / % possible obs: 99.5 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 / Χ2: 0.85 / Net I/σ(I): 11.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 43.53 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SHT Resolution: 2.1→45.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2394 / WRfactor Rwork: 0.1959 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8437 / SU B: 4.066 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1851 / SU Rfree: 0.1709 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.65 Å2 / Biso mean: 33.1432 Å2 / Biso min: 11.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→45.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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