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Yorodumi- PDB-3n5u: Crystal structure of an Rb C-terminal peptide bound to the cataly... -
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-Basic information
Entry | Database: PDB / ID: 3n5u | ||||||
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Title | Crystal structure of an Rb C-terminal peptide bound to the catalytic subunit of PP1 | ||||||
Components |
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Keywords | HYDROLASE / TRANSCRIPTION REGULATION / Retinoblastoma / pRb / Rb / protein phosphatase-1 / PP1 / phosphatase | ||||||
Function / homology | Function and homology information Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / regulation of glycogen catabolic process / sister chromatid biorientation / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / telomere maintenance in response to DNA damage / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / regulation of centromere complex assembly / Aberrant regulation of mitotic exit in cancer due to RB1 defects / positive regulation of macrophage differentiation / positive regulation of transcription regulatory region DNA binding / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / glial cell apoptotic process / tissue homeostasis / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / positive regulation of mitotic metaphase/anaphase transition / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / digestive tract development / aortic valve morphogenesis / regulation of canonical Wnt signaling pathway / Replication of the SARS-CoV-1 genome / myoblast differentiation / negative regulation of cold-induced thermogenesis / SWI/SNF complex / regulation of translational initiation / Cyclin E associated events during G1/S transition / negative regulation of glial cell proliferation / myosin phosphatase activity / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / hepatocyte apoptotic process / dephosphorylation / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / Cyclin A:Cdk2-associated events at S phase entry / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / regulation of mitotic cell cycle / phosphatase activity / phosphoprotein phosphatase activity / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / DARPP-32 events / chromosome organization / glial cell proliferation / chondrocyte differentiation / Nuclear events stimulated by ALK signaling in cancer / ribonucleoprotein complex binding / negative regulation of smoothened signaling pathway / epithelial cell proliferation / striated muscle cell differentiation / protein dephosphorylation / Condensation of Prophase Chromosomes / Downregulation of TGF-beta receptor signaling / lung development / regulation of circadian rhythm / phosphoprotein binding / adherens junction / RNA polymerase II transcription regulatory region sequence-specific DNA binding / kinase binding / response to lead ion / negative regulation of protein kinase activity / negative regulation of inflammatory response / circadian regulation of gene expression / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cyclin D associated events in G1 / negative regulation of DNA-binding transcription factor activity / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / heterochromatin formation / PML body / negative regulation of cell growth / spindle / cellular response to xenobiotic stimulus / transcription corepressor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å | ||||||
Authors | Hirschi, A.M. / Cecchini, M. / Steinhardt, R.C. / Dick, F.A. / Rubin, S.M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: An overlapping kinase and phosphatase docking site regulates activity of the retinoblastoma protein. Authors: Hirschi, A. / Cecchini, M. / Steinhardt, R.C. / Schamber, M.R. / Dick, F.A. / Rubin, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n5u.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n5u.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 3n5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n5u_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 3n5u_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 3n5u_validation.xml.gz | 23 KB | Display | |
Data in CIF | 3n5u_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/3n5u ftp://data.pdbj.org/pub/pdb/validation_reports/n5/3n5u | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 7 - 300 / Label seq-ID: 7 - 300
NCS oper: (Code: given Matrix: (-0.386983, 0.921948, -0.016028), Vector: |
-Components
#1: Protein | Mass: 34370.359 Da / Num. of mol.: 2 / Fragment: UNP residues 1-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1A, PPP1CA / Plasmid: pFLAG-CTS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P62136, protein-serine/threonine phosphatase #2: Protein/peptide | | Mass: 1534.842 Da / Num. of mol.: 1 / Fragment: UNP residues 870-882 / Source method: obtained synthetically / Details: synthetic 13-mer peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P06400 #3: Chemical | ChemComp-MN / #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: 3.04 Å3/Da / Density % sol: 59.56 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 7.5 Details: 100mM HEPES, 200mM MgCl2, 18% PEG 4000, pH 7.5, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2009 |
Radiation | Monochromator: ASSYMETRIC CURVED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→83 Å / Num. obs: 13588 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→83 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.45 / σ(F): 0.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.556 Å2 / ksol: 0.342 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.86 Å2 / Biso mean: 53.969 Å2 / Biso min: 27.02 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→83 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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