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Open data
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Basic information
Entry | Database: PDB / ID: 3c9c | ||||||
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Title | Structural Basis of Histone H4 Recognition by p55 | ||||||
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![]() | TRANSCRIPTION REPRESSOR / p55 / chromatin / epigenetics / WD4 / histone / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / WD repeat / Chromosomal protein / DNA-binding / Nucleosome core / NUCLEAR PROTEIN | ||||||
Function / homology | ![]() G0 and Early G1 / Regulation of TP53 Activity through Acetylation / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex ...G0 and Early G1 / Regulation of TP53 Activity through Acetylation / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / eggshell chorion gene amplification / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Myb complex / Oxidative Stress Induced Senescence / segment specification / CAF-1 complex / Rpd3L complex / Rpd3L-Expanded complex / facultative heterochromatin formation / polytene chromosome / NURF complex / nucleosome organization / DNA replication-dependent chromatin assembly / NuRD complex / ESC/E(Z) complex / histone methyltransferase complex / nuclear chromosome / Sin3-type complex / heterochromatin formation / nucleosome binding / regulation of mitotic cell cycle / histone deacetylase binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / chromosome / histone binding / transcription regulator complex / nucleic acid binding / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, J.J. / Garlick, J.D. / Kingston, R.E. | ||||||
![]() | ![]() Title: Structural basis of histone H4 recognition by p55. Authors: Song, J.J. / Garlick, J.D. / Kingston, R.E. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.7 KB | Display | ![]() |
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PDB format | ![]() | 64.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
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Full document | ![]() | 460.2 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c99SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48817.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3191.853 Da / Num. of mol.: 1 / Fragment: UNP residues 16-42 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence is found naturally in Drosophila melanogaster. References: UniProt: P84040 |
#3: Chemical | ChemComp-CD / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.219 Å3/Da / Density % sol: 80.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 21402 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.591 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3c99 Resolution: 3.2→50 Å
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Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
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Refine LS restraints |
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