+Open data
-Basic information
Entry | Database: PDB / ID: 7smf | ||||||
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Title | p107 pocket domain complexed with mutated HDAC1-3X peptide | ||||||
Components |
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Keywords | CELL CYCLE / Transcription / cyclin box pocket transcriptional regulator | ||||||
Function / homology | Function and homology information regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / G0 and Early G1 / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / G0 and Early G1 / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Cyclin D associated events in G1 / chromatin organization / transcription regulator complex / cell differentiation / negative regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Putta, S. / Fernandez, S.M. / Tripathi, S.M. / Muller, G.A. / Rubin, S.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2022 Title: Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family. Authors: Putta, S. / Alvarez, L. / Ludtke, S. / Sehr, P. / Muller, G.A. / Fernandez, S.M. / Tripathi, S. / Lewis, J. / Gibson, T.J. / Chemes, L.B. / 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 | 7smf.cif.gz | 298.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7smf.ent.gz | 240.2 KB | Display | PDB format |
PDBx/mmJSON format | 7smf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7smf_validation.pdf.gz | 463.7 KB | Display | wwPDB validaton report |
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Full document | 7smf_full_validation.pdf.gz | 472.4 KB | Display | |
Data in XML | 7smf_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 7smf_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/7smf ftp://data.pdbj.org/pub/pdb/validation_reports/sm/7smf | HTTPS FTP |
-Related structure data
Related structure data | 7smcC 7smdC 7smeC 4yosS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43265.965 Da / Num. of mol.: 2 / Fragment: UNP residues 391-601,780-887,924-972 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28749 #2: Protein/peptide | Mass: 1283.318 Da / Num. of mol.: 2 / Fragment: UNP residues 413-422 / Mutation: R413D, A415Y, E417Y / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: histone deacetylase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.34 Å3/Da / Density % sol: 63.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3→39.29 Å / Num. obs: 21589 / % possible obs: 93.5 % / Redundancy: 2 % / CC1/2: 0.81 / Rmerge(I) obs: 0.251 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 3→3.18 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3425 / CC1/2: 0.64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4YOS Resolution: 3→39.29 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.8 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.29 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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