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Yorodumi- PDB-2azm: Crystal structure of the MDC1 brct repeat in complex with the his... -
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-Basic information
Entry | Database: PDB / ID: 2azm | ||||||
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Title | Crystal structure of the MDC1 brct repeat in complex with the histone tail of gamma-H2AX | ||||||
Components |
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Keywords | CELL CYCLE / BRCT REPEAT / PROTEIN-PHOSPHOPEPTIDE COMPLEX / DNA DAMAGE | ||||||
Function / homology | Function and homology information XY body / protein localization to site of double-strand break / DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / response to ionizing radiation / site of DNA damage / positive regulation of transcription initiation by RNA polymerase II / Replacement of protamines by nucleosomes in the male pronucleus / SUMOylation of DNA damage response and repair proteins / Packaging Of Telomere Ends ...XY body / protein localization to site of double-strand break / DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / response to ionizing radiation / site of DNA damage / positive regulation of transcription initiation by RNA polymerase II / Replacement of protamines by nucleosomes in the male pronucleus / SUMOylation of DNA damage response and repair proteins / 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 / Inhibition of DNA recombination at telomere / positive regulation of DNA repair / Meiotic synapsis / histone reader activity / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / replication fork / 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 / TP53 Regulates Transcription of DNA Repair Genes / 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 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / 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 / cellular senescence / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / damaged DNA binding / nuclear body / nuclear speck / protein heterodimerization activity / Amyloid fiber formation / focal adhesion / DNA repair / centrosome / DNA damage response / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å | ||||||
Authors | Clapperton, J.A. / Stucki, M. / Mohammad, D. / Yaffe, M.B. / Jackson, S.P. / Smerdon, S.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2005 Title: MDC1 Directly Binds Phosphorylated Histone H2AX to Regulate Cellular Responses to DNA Double-Strand Breaks Authors: Stucki, M. / Clapperton, J.A. / Mohammad, D. / Yaffe, M.B. / Smerdon, S.J. / Jackson, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2azm.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2azm.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 2azm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/2azm ftp://data.pdbj.org/pub/pdb/validation_reports/az/2azm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22884.963 Da / Num. of mol.: 2 / Fragment: BRCT REPEAT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDC1 / Plasmid: PGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q14676 #2: Protein/peptide | Mass: 1235.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GAMMA H2AX SYNTHETIC PEPTIDE / References: UniProt: P16104*PLUS #3: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, NaCl, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97852 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 23006 / Num. obs: 23006 / Redundancy: 12.6 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.4→2.51 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.41→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.155 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.541 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.471 Å / Total num. of bins used: 20
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