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Yorodumi- PDB-1o9k: Crystal structure of the retinoblastoma tumour suppressor protein... -
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-Basic information
Entry | Database: PDB / ID: 1o9k | ||||||
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Title | Crystal structure of the retinoblastoma tumour suppressor protein bound to E2F peptide | ||||||
Components |
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Keywords | APOPTOSIS / TUMOUR SUPPRESSOR / CELL CYCLE REGULATION / DNA-BINDING | ||||||
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 / lens fiber cell apoptotic process / regulation of lipid kinase activity / negative regulation of fat cell proliferation / negative regulation of myofibroblast 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 / lens fiber cell apoptotic process / regulation of lipid kinase activity / negative regulation of fat cell proliferation / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / G2 Phase / 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 / 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 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / negative regulation of hepatocyte apoptotic process / neuron maturation / Transcription of E2F targets under negative control by DREAM complex / digestive tract development / mRNA stabilization / aortic valve morphogenesis / Activation of NOXA and translocation to mitochondria / anoikis / Replication of the SARS-CoV-1 genome / myoblast differentiation / negative regulation of cold-induced thermogenesis / SWI/SNF complex / Activation of PUMA and translocation to mitochondria / Cyclin E associated events during G1/S transition / negative regulation of glial cell proliferation / DNA-binding transcription activator activity / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / negative regulation of fat cell differentiation / G1/S-Specific Transcription / hepatocyte apoptotic process / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of DNA binding / skeletal muscle cell differentiation / Transcriptional Regulation by E2F6 / RUNX2 regulates osteoblast differentiation / regulation of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cell cycle / chromosome organization / glial cell proliferation / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / forebrain development / epithelial cell proliferation / striated muscle cell differentiation / Condensation of Prophase Chromosomes / DNA damage checkpoint signaling / Transcriptional regulation of granulopoiesis / phosphoprotein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / kinase binding / negative regulation of protein kinase activity / negative regulation of inflammatory response / 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 / RNA polymerase II transcription regulator complex / Pre-NOTCH Transcription and Translation / positive regulation of fibroblast proliferation / spindle / cellular response to xenobiotic stimulus / transcription corepressor activity / negative regulation of epithelial cell proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / disordered domain specific binding / neuron projection development / sequence-specific double-stranded DNA binding / Replication of the SARS-CoV-2 genome Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Xiao, B. / Spencer, J. / Clements, A. / Ali-Khan, N. / Mittnacht, S. / Broceno, C. / Burghammer, M. / Perrakis, A. / Marmorstein, R. / Gamblin, S.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Crystal Structure of the Retinoblastoma Tumor Suppressor Protein Bound to E2F and the Molecular Basis of its Regulation Authors: Xiao, B. / Spencer, J. / Clements, A. / Ali-Khan, N. / Mittnacht, S. / Broceno, C. / Burghammer, M. / Perrakis, A. / Marmorstein, R. / Gamblin, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9k.cif.gz | 296.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9k.ent.gz | 243 KB | Display | PDB format |
PDBx/mmJSON format | 1o9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o9k_validation.pdf.gz | 517.2 KB | Display | wwPDB validaton report |
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Full document | 1o9k_full_validation.pdf.gz | 587.7 KB | Display | |
Data in XML | 1o9k_validation.xml.gz | 59.3 KB | Display | |
Data in CIF | 1o9k_validation.cif.gz | 81.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9k ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9k | HTTPS FTP |
-Related structure data
Related structure data | 1guxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25100.910 Da / Num. of mol.: 4 / Fragment: DOMAIN A, RESIDUES 372-589 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P06400 #2: Protein | Mass: 18265.477 Da / Num. of mol.: 4 / Fragment: DOMAIN B, RESIDUES 636-787 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P06400 #3: Protein/peptide | Mass: 2127.269 Da / Num. of mol.: 4 / Fragment: RESIDUES 409-426 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q01094 #4: Water | ChemComp-HOH / | Compound details | RETINOBLASTOMA-ASSOCIATED PROTEIN: REGULATOR OF OTHER GENES. ACTS AS A TUMOR SUPPRESSOR. INTERACTS ...RETINOBLAS | |
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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: 2.45 Å3/Da / Density % sol: 49.84 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: pH 7.80 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 85 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 53846 / % possible obs: 88.1 % / Redundancy: 8.8 % / Rsym value: 0.094 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.6→2.69 Å |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GUX Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.823 / SU B: 13.486 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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