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Yorodumi- PDB-1k2m: Solution Structure of the FHA2 Domain of Rad53 Complexed with a P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k2m | |||||||||
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Title | Solution Structure of the FHA2 Domain of Rad53 Complexed with a Phosphotyrosyl Peptide Derived from Rad9 | |||||||||
Components |
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Keywords | TRANSFERASE / FHA domain / Rad53 / Rad9 / Phosphotyrosine / phosphoprotein | |||||||||
Function / homology | Function and homology information deoxyribonucleoside triphosphate biosynthetic process / negative regulation of DNA strand resection involved in replication fork processing / meiotic recombination checkpoint signaling / telomere maintenance in response to DNA damage / SUMOylation of transcription factors / negative regulation of phosphorylation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase / mitotic intra-S DNA damage checkpoint signaling / DNA replication origin binding ...deoxyribonucleoside triphosphate biosynthetic process / negative regulation of DNA strand resection involved in replication fork processing / meiotic recombination checkpoint signaling / telomere maintenance in response to DNA damage / SUMOylation of transcription factors / negative regulation of phosphorylation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase / mitotic intra-S DNA damage checkpoint signaling / DNA replication origin binding / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / enzyme activator activity / mitotic G1 DNA damage checkpoint signaling / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / nucleotide-excision repair / protein localization / double-strand break repair / histone binding / double-stranded DNA binding / protein tyrosine kinase activity / regulation of cell cycle / protein kinase activity / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Byeon, I.-J.L. / Yongkiettrakul, S. / Tsai, M.-D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Solution structure of the yeast Rad53 FHA2 complexed with a phosphothreonine peptide pTXXL: comparison with the structures of FHA2-pYXL and FHA1-pTXXD complexes. Authors: Byeon, I.J. / Yongkiettrakul, S. / Tsai, M.D. #1: Journal: J.Mol.Biol. / Year: 2000 Title: II. Structure and Specificity of the Interaction between the FHA2 Domain of Rad53 and Phosphotyrosyl Peptides. Authors: Wang, P. / Byeon, I.J. / Liao, H. / Beebe, K.D. / Yongkiettrakul, S. / Pei, D. / Tsai, M.D. #2: Journal: J.Mol.Biol. / Year: 1999 Title: Structure and Function of a New Phosphopeptide-binding Domain Containing the FHA2 of Rad53. Authors: Liao, H. / Byeon, I.J. / Tsai, M.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k2m.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1k2m.ent.gz | 957.9 KB | Display | PDB format |
PDBx/mmJSON format | 1k2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k2m_validation.pdf.gz | 363.8 KB | Display | wwPDB validaton report |
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Full document | 1k2m_full_validation.pdf.gz | 636.2 KB | Display | |
Data in XML | 1k2m_validation.xml.gz | 102.8 KB | Display | |
Data in CIF | 1k2m_validation.cif.gz | 127.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/1k2m ftp://data.pdbj.org/pub/pdb/validation_reports/k2/1k2m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18148.758 Da / Num. of mol.: 1 / Fragment: C-terminal FHA domain (FHA2) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPK1 or RAD53 / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P22216, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Protein/peptide | Mass: 1009.947 Da / Num. of mol.: 1 / Fragment: residues 826-832 / Source method: obtained synthetically Details: This phosphotyrosyl peptide was chemically synthesized. References: UniProt: P14737 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 0.5 mM FHA2 U-15N,13C; 1mM phosphotyrosyl peptide of Rad9; 10 mM sodium phosphate (pH 6.5), 1 mM DTT, and 1 mM EDTA Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 10 mM sodium phosphate(pH 6.5), 1 mM DTT, and 1 mM EDTA pH: 6.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The complex structures are generated using a total of 3398 restraints, 3210 distance restraints, and 188 TOLOS-derived dihedral angle restraints. | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 22 |