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Yorodumi- PDB-5t2s: Structure of the FHA1 domain of Rad53 bound simultaneously to the... -
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-Basic information
Entry | Database: PDB / ID: 5t2s | ||||||
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Title | Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide. | ||||||
Components |
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Keywords | CELL CYCLE / FHA / BRCT / phosphopeptide / protein chimera | ||||||
Function / homology | Function and homology information positive regulation of spindle attachment to meiosis I kinetochore / positive regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / deoxyribonucleoside triphosphate biosynthetic process / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / regulation of cell cycle phase transition ...positive regulation of spindle attachment to meiosis I kinetochore / positive regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / deoxyribonucleoside triphosphate biosynthetic process / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / meiotic recombination checkpoint signaling / mitotic DNA damage checkpoint signaling / mitotic DNA replication preinitiation complex assembly / premeiotic DNA replication / Activation of the pre-replicative complex / negative regulation of phosphorylation / Activation of ATR in response to replication stress / protein-containing complex localization / mitotic DNA replication checkpoint signaling / dual-specificity kinase / double-strand break repair via break-induced replication / calmodulin-dependent protein kinase activity / DNA replication origin binding / negative regulation of DNA damage checkpoint / chromosome, centromeric region / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / DNA damage checkpoint signaling / chromosome segregation / protein localization / cellular response to oxidative stress / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / positive regulation of protein phosphorylation / phosphorylation / cell division / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / signal transduction / zinc ion binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Guarne, A. / Almawi, A. / Matthews, L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: 'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7. Authors: Almawi, A.W. / Matthews, L.A. / Myrox, P. / Boulton, S. / Lai, C. / Moraes, T. / Melacini, G. / Ghirlando, R. / Duncker, B.P. / Guarne, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t2s.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t2s.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 5t2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t2s_validation.pdf.gz | 457.8 KB | Display | wwPDB validaton report |
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Full document | 5t2s_full_validation.pdf.gz | 459.5 KB | Display | |
Data in XML | 5t2s_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5t2s_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/5t2s ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t2s | HTTPS FTP |
-Related structure data
Related structure data | 5t2fC 1g6gS 3qbzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30571.002 Da / Num. of mol.: 2 Fragment: UNP P32325 residues 105-220 linked to UNP P22216 residues 22-162 via LINKER residues VDGS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c Gene: DBF4, DNA52, YDR052C, D4205, YD9609.07C, RAD53, MEC2, SAD1, SPK1, YPL153C, P2588 Plasmid: modified pET15b Details (production host): Contains aTEV-removable His6-SUMO tag Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P32325, UniProt: P22216, dual-specificity kinase #2: Protein/peptide | Mass: 1347.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: short phosphorylated peptide derived from Cdc7 / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06243*PLUS #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM TRIS pH 8.5 12.5 % PEG 3350 (v/v) / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 4, 2015 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→39.674 Å / Num. obs: 36580 / % possible obs: 98.3 % / Redundancy: 2.8 % / CC1/2: 0.99 / Net I/σ(I): 8.15 |
Reflection shell | Resolution: 2.2→2.6 Å / Redundancy: 2.8 % / CC1/2: 0.318 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G6G; 3QBZ Resolution: 2.4→39.674 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.674 Å
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Refine LS restraints |
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LS refinement shell |
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