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Yorodumi- PDB-1k3n: NMR Structure of the FHA1 Domain of Rad53 in Complex with a Rad9-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k3n | ||||||
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Title | NMR Structure of the FHA1 Domain of Rad53 in Complex with a Rad9-derived Phosphothreonine (at T155) Peptide | ||||||
Components |
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Keywords | TRANSFERASE/CELL CYCLE / FHA domain / Rad53 / rad9 / phosphothreonine / phosphoprotein / TRANSFERASE-CELL CYCLE COMPLEX | ||||||
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 / The complex structures are generated using a total of 2438 restraints. Among them, 3 artifical constraints, 192 TALOS-derived dihedral angle restrains, 78 restraints from H-bond, 16 intermolecular distance constrains, and 2149 intra-FHA1, intra-peptide distance constraints. | ||||||
Authors | Yuan, C. / Yongkiettrakul, S. / Byeon, I.-J.L. / Zhou, S. / Tsai, M.-D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Solution structures of two FHA1-phosphothreonine peptide complexes provide insight into the structural basis of the ligand specificity of FHA1 from yeast Rad53. Authors: Yuan, C. / Yongkiettrakul, S. / Byeon, I.J. / Zhou, S. / Tsai, M.D. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Structure of the FHA1 Domain of Yeast Rad53 and Identification of Binding Sites for Both FHA1 and Its Target Protein Rad9. Authors: Liao, H. / Yuan, C. / Su, M.I. / Yongkiettrakul, S. / Qin, D. / Li, H. / Byeon, I.J. / Pei, D. / 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 | 1k3n.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1k3n.ent.gz | 898.9 KB | Display | PDB format |
PDBx/mmJSON format | 1k3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k3n_validation.pdf.gz | 363 KB | Display | wwPDB validaton report |
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Full document | 1k3n_full_validation.pdf.gz | 614.5 KB | Display | |
Data in XML | 1k3n_validation.xml.gz | 84.1 KB | Display | |
Data in CIF | 1k3n_validation.cif.gz | 102.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/1k3n ftp://data.pdbj.org/pub/pdb/validation_reports/k3/1k3n | 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: 17093.490 Da / Num. of mol.: 1 / Fragment: N-terminal FHA domain (FHA1) 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: 1617.754 Da / Num. of mol.: 1 / Fragment: Residues 149-161 / Source method: obtained synthetically Details: This phosphothreonine 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 FHA1 U-15N,13C; 10 mM sodium phosphate buffer (pH 6.5), 1mM DTT, and 1 mM EDTA; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 10 mM sodium phosphate, 1mM 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: The complex structures are generated using a total of 2438 restraints. Among them, 3 artifical constraints, 192 TALOS-derived dihedral angle restrains, 78 restraints from H-bond, 16 ...Method: The complex structures are generated using a total of 2438 restraints. Among them, 3 artifical constraints, 192 TALOS-derived dihedral angle restrains, 78 restraints from H-bond, 16 intermolecular distance constrains, and 2149 intra-FHA1, intra-peptide distance constraints. Software ordinal: 1 | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |