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- PDB-1k3q: NMR structure of the FHA1 Domain of Rad53 in Complex with a Rad9-... -
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Basic information
Entry | Database: PDB / ID: 1k3q | ||||||
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Title | NMR structure of the FHA1 Domain of Rad53 in Complex with a Rad9-derived Phosphothreonine (at T192) Peptide | ||||||
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![]() | TRANSFERASE/CELL CYCLE / FHA domain / Rad53 / Rad9 / phosphothreonine / phosphoprotein / TRANSFERASE-CELL CYCLE COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | SOLUTION NMR / The complex structure are generated using a total of 2474 restraints. Among them, 3 artificial constraints, 192 TALOS-derived dihedral angle restraints, 78 H-bond restraints, 22 intermolecular distance constrains, and 2179 intra-FHA1, intra-peptide distance constraints | ||||||
![]() | Yuan, C. / Yongkiettrakul, S. / Byeon, I.-J.L. / Zhou, S. / Tsai, M.-D. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 888.3 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 362.4 KB | Display | ![]() |
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Full document | ![]() | 615.1 KB | Display | |
Data in XML | ![]() | 85.1 KB | Display | |
Data in CIF | ![]() | 104 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: SPK1 or Rad53 / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P22216, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Protein/peptide | Mass: 1489.474 Da / Num. of mol.: 1 / Fragment: Residues 188-200 / 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 |
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Sample preparation
Details | Contents: 0.5 mM FHA1 U-15N,13C; 10 mM sodium phosphate buffer (pH 6.5), 1 mM 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, 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 |
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Processing
NMR software |
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Refinement | Method: The complex structure are generated using a total of 2474 restraints. Among them, 3 artificial constraints, 192 TALOS-derived dihedral angle restraints, 78 H-bond restraints, 22 ...Method: The complex structure are generated using a total of 2474 restraints. Among them, 3 artificial constraints, 192 TALOS-derived dihedral angle restraints, 78 H-bond restraints, 22 intermolecular distance constrains, and 2179 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 |