[English] 日本語
Yorodumi- PDB-2a0t: NMR structure of the FHA1 domain of Rad53 in complex with a biolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a0t | ||||||
---|---|---|---|---|---|---|---|
Title | NMR structure of the FHA1 domain of Rad53 in complex with a biological relevant phosphopeptide derived from Madt1 | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / FHA domain. Rad53 / Mdt1 / phosphothreonine / phosphoprotein | ||||||
Function / homology | Function and homology information regulation of mRNA stability involved in response to oxidative stress / deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / negative regulation of phosphorylation / dual-specificity kinase / poly(A)+ mRNA export from nucleus / telomere maintenance in response to DNA damage / DNA replication origin binding ...regulation of mRNA stability involved in response to oxidative stress / deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / negative regulation of phosphorylation / dual-specificity kinase / poly(A)+ mRNA export from nucleus / telomere maintenance in response to DNA damage / DNA replication origin binding / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / G2/M transition of mitotic cell cycle / protein localization / protein tyrosine kinase activity / protein kinase activity / ribonucleoprotein complex / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Mahajan, A. / Yuan, C. / Pike, B.L. / Heierhorst, J. / Chang, C.-F. / Tsai, M.-D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: FHA Domain-Ligand Interactions: Importance of Integrating Chemical and Biological Approaches Authors: Mahajan, A. / Yuan, C. / Pike, B.L. / Heierhorst, J. / Chang, C.-F. / Tsai, M.-D. #1: 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.L. / Zhou, S. / Tsai, M.-D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a0t.cif.gz | 1005.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a0t.ent.gz | 868.9 KB | Display | PDB format |
PDBx/mmJSON format | 2a0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a0t_validation.pdf.gz | 357.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2a0t_full_validation.pdf.gz | 614.5 KB | Display | |
Data in XML | 2a0t_validation.xml.gz | 86.9 KB | Display | |
Data in CIF | 2a0t_validation.cif.gz | 106.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/2a0t ftp://data.pdbj.org/pub/pdb/validation_reports/a0/2a0t | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-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, EC: 2.7.1.37 |
---|---|
#2: Protein/peptide | Mass: 1246.173 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in Saccharomyces cerevisiae (yeast) References: UniProt: P34217 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||
NMR spectrometer |
|
-Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: The complex structures are generated using a total of 2524 NMR constraints including constraints in this PDB file and constraints of free FHA1 in PDB access code 1K3J | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average, lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |