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Yorodumi- PDB-3u3z: Structure of human microcephalin (MCPH1) tandem BRCT domains in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u3z | ||||||
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Title | Structure of human microcephalin (MCPH1) tandem BRCT domains in complex with an H2A.X peptide phosphorylated at Ser139 and Tyr142 | ||||||
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Keywords | CELL CYCLE / DNA repair / cell cycle regulation | ||||||
Function / homology | Function and homology information regulation of chromosome condensation / chromatin-protein adaptor activity / neuronal stem cell population maintenance / regulation of centrosome cycle / XY body / protein localization to site of double-strand break / protein localization to centrosome / response to ionizing radiation / establishment of mitotic spindle orientation / site of DNA damage ...regulation of chromosome condensation / chromatin-protein adaptor activity / neuronal stem cell population maintenance / regulation of centrosome cycle / XY body / protein localization to site of double-strand break / protein localization to centrosome / response to ionizing radiation / establishment of mitotic spindle orientation / site of DNA damage / condensed nuclear chromosome / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of DNA repair / Packaging Of Telomere Ends / meiotic cell cycle / male germ cell nucleus / 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 / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / DNA damage checkpoint signaling / replication fork / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / double-strand break repair via homologous recombination / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / bone development / B-WICH complex positively regulates rRNA expression / heterochromatin formation / cellular senescence / cellular response to gamma radiation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / cerebral cortex development / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / double-strand break repair / Processing of DNA double-strand break ends / regulation of inflammatory response / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / mitotic cell cycle / site of double-strand break / histone binding / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / damaged DNA binding / nuclear speck / protein heterodimerization activity / Amyloid fiber formation / centrosome / DNA damage response / enzyme binding / negative regulation of transcription by RNA polymerase II / 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 / Resolution: 1.5 Å | ||||||
Authors | Singh, N. / Thompson, J.R. / Heroux, A. / Mer, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1. Authors: Singh, N. / Basnet, H. / Wiltshire, T.D. / Mohammad, D.H. / Thompson, J.R. / Heroux, A. / Botuyan, M.V. / Yaffe, M.B. / Couch, F.J. / Rosenfeld, M.G. / Mer, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u3z.cif.gz | 139.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u3z.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 3u3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u3z_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
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Full document | 3u3z_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 3u3z_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3u3z_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/3u3z ftp://data.pdbj.org/pub/pdb/validation_reports/u3/3u3z | HTTPS FTP |
-Related structure data
Related structure data | 3szmSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21949.551 Da / Num. of mol.: 1 Fragment: Tandem BRCT domains (BRCT2-BRCT3, UNP residues 640-835) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: PTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA (DE3) / References: UniProt: Q8NEM0 | ||
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#2: Protein/peptide | Mass: 685.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104*PLUS | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 22% PEG3350, 0.03 M citric acid, 0.07 M Bis-Tris-propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2010 |
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 29928 / % possible obs: 96.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.3 / % possible all: 80.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SZM Resolution: 1.5→23.79 Å / SU ML: 0.16 / σ(F): 1.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9061 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→23.79 Å
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Refine LS restraints |
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LS refinement shell |
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