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Yorodumi- PDB-3unn: Monomeric structure of the human MDC1 FHA domain in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3unn | ||||||
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Title | Monomeric structure of the human MDC1 FHA domain in complex with an MDC1 phospho-T4 peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / FHA / Phosphoprotein binding | ||||||
Function / homology | Function and homology information chromatin-protein adaptor activity / DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...chromatin-protein adaptor activity / DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / site of double-strand break / Processing of DNA double-strand break ends / nuclear body / DNA repair / focal adhesion / DNA damage response / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Luo, S. / Ye, K. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain Authors: Liu, J. / Luo, S. / Zhao, H. / Liao, J. / Li, J. / Yang, C. / Xu, B. / Stern, D.F. / Xu, X. / Ye, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3unn.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3unn.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 3unn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3unn_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 3unn_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 3unn_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 3unn_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/3unn ftp://data.pdbj.org/pub/pdb/validation_reports/un/3unn | HTTPS FTP |
-Related structure data
Related structure data | 3umzSC 3unmC 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: 12509.480 Da / Num. of mol.: 1 / Fragment: FHA domain, residues 27-138 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDC1, KIAA0170, NFBD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14676 |
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#2: Protein/peptide | Mass: 1001.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14676 |
#3: 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: 2.43 Å3/Da / Density % sol: 49.42 % / Mosaicity: 0.455 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.2M Ammonium acetate, 0.1M HEPES, 57% MPD, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.96396 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 9, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96396 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→45 Å / Num. obs: 14992 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.046 / Χ2: 1.426 / Net I/σ(I): 14.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UMZ Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.88 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.106 / 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: 51.16 Å2 / Biso mean: 21.4101 Å2 / Biso min: 11.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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