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Yorodumi- PDB-2pmi: Structure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pmi | ||||||
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Title | Structure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-responsive Signal Transduction Pathway with Bound ATP-gamma-S | ||||||
Components |
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Keywords | SIGNALING PROTEIN / TRANSFERASE/CELL CYCLE / cyclin-dependent kinase / cyclin / TRANSFERASE-CELL CYCLE COMPLEX | ||||||
Function / homology | Function and homology information establishment or maintenance of cytoskeleton polarity / Pho85-Pho80 CDK-cyclin complex / negative regulation of phosphate metabolic process / regulation of establishment or maintenance of cell polarity / negative regulation of calcium-mediated signaling / regulation of cell cycle phase transition / vacuole fusion, non-autophagic / long-chain fatty acid metabolic process / positive regulation of phospholipid biosynthetic process / fungal-type cell wall organization ...establishment or maintenance of cytoskeleton polarity / Pho85-Pho80 CDK-cyclin complex / negative regulation of phosphate metabolic process / regulation of establishment or maintenance of cell polarity / negative regulation of calcium-mediated signaling / regulation of cell cycle phase transition / vacuole fusion, non-autophagic / long-chain fatty acid metabolic process / positive regulation of phospholipid biosynthetic process / fungal-type cell wall organization / regulation of glycogen biosynthetic process / regulation of nucleocytoplasmic transport / intracellular monoatomic cation homeostasis / negative regulation of glycogen biosynthetic process / cell cycle G1/S phase transition / cellular bud neck / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of macroautophagy / regulation of cell division / lipid homeostasis / positive regulation of macroautophagy / regulation of lipid metabolic process / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / G1/S transition of mitotic cell cycle / regulation of protein stability / regulation of protein localization / regulation of cell cycle / protein kinase activity / phosphorylation / protein serine kinase activity / DNA damage response / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huang, K. / Ferrin-O'Connell, I. / Zhang, W. / Leonard, G.A. / O'Shea, E.K. / Quiocho, F.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: Structure of the Pho85-Pho80 CDK-Cyclin Complex of the Phosphate-Responsive Signal Transduction Pathway Authors: Huang, K. / Ferrin-O'Connell, I. / Zhang, W. / Leonard, G.A. / O'Shea, E.K. / Quiocho, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pmi.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pmi.ent.gz | 170.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/2pmi ftp://data.pdbj.org/pub/pdb/validation_reports/pm/2pmi | HTTPS FTP |
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-Related structure data
Related structure data | 2pk9SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a heterodimer. The asymmetric unit is composed of two heterodimers. The coordinates contain both heterodimers in the asymmetric unit. |
-Components
#1: Protein | Mass: 36356.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PHO85, SSG3 / Plasmid: pQE60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P17157, cyclin-dependent kinase #2: Protein | Mass: 33273.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PHO80, AGS3, TUP7, VAC5 / Plasmid: pSBET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P20052 #3: Chemical | ChemComp-AGS / | #4: Chemical | |
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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: 4.74 Å3/Da / Density % sol: 74.04 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 9ul 12% PEG 10000, 10% glycerol, 0.05 M strontium chloride (SrCl2), 10 mM Tris (2-carboxyethyl) phosphine (TCEP, 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.5, VAPOR DIFFUSION, HANGING ...Details: 9ul 12% PEG 10000, 10% glycerol, 0.05 M strontium chloride (SrCl2), 10 mM Tris (2-carboxyethyl) phosphine (TCEP, 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2006 / Details: APS 19ID |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→14.98 Å / Num. all: 53704 / Num. obs: 53704 / % possible obs: 91.1 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.248 / % possible all: 75.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PK9 Resolution: 2.9→14.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 97128.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.7203 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→14.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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