+Open data
-Basic information
Entry | Database: PDB / ID: 2f8n | ||||||
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Title | 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / Nucleosome / NCP / macroH2A / Histone variant / chromatin / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / negative regulation of response to oxidative stress / regulation of response to oxidative stress / Barr body / ADP-D-ribose binding / Deposition of new CENPA-containing nucleosomes at the centromere ...negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / negative regulation of response to oxidative stress / regulation of response to oxidative stress / Barr body / ADP-D-ribose binding / Deposition of new CENPA-containing nucleosomes at the centromere / Condensation of Prophase Chromosomes / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / ADP-D-ribose modification-dependent protein binding / sex-chromosome dosage compensation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs / sex chromatin / UCH proteinases / PRC2 methylates histones and DNA / HATs acetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / establishment of protein localization to chromatin / positive regulation of endodermal cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / double-stranded methylated DNA binding / rDNA binding / Estrogen-dependent gene expression / regulation of oxidative phosphorylation / negative regulation of protein serine/threonine kinase activity / Ub-specific processing proteases / poly-ADP-D-ribose modification-dependent protein binding / protein serine/threonine kinase inhibitor activity / positive regulation of keratinocyte differentiation / nucleosomal DNA binding / negative regulation of gene expression, epigenetic / nuclear chromosome / site of DNA damage / regulation of lipid metabolic process / pericentric heterochromatin / epigenetic regulation of gene expression / condensed chromosome / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / DNA repair / chromatin / nucleolus / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Chakravarthy, S. / Luger, K. | ||||||
Citation | Journal: To be Published Title: Nucleosomes containing the histone domain of macroH2A: In vitro possibilities. Authors: Chakravarthy, S. / Luger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f8n.cif.gz | 320.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f8n.ent.gz | 244.8 KB | Display | PDB format |
PDBx/mmJSON format | 2f8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/2f8n ftp://data.pdbj.org/pub/pdb/validation_reports/f8/2f8n | HTTPS FTP |
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-Related structure data
Related structure data | 1u35S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is an octamer of histones wrapped by 146 basepairs of DNA called the nucleosome core particle, which is also the asymmetric unit. (all of which, the coordinates are given for in the submitted pdb file). |
-Components
-Protein , 6 types, 8 molecules AEBFDHGK
#2: Protein | Mass: 15421.101 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: P84233 #3: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: P62799 #4: Protein | | Mass: 14025.280 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: Q9D2U9 #5: Protein | | Mass: 13655.948 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: P02281 #6: Protein | | Mass: 12984.343 Da / Num. of mol.: 1 / Fragment: residues 0-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: O75367 #7: Protein | | Mass: 16198.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: Q8CGP6 |
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-DNA chain / Non-polymers , 2 types, 122 molecules IJ
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: puc19 / Production host: Escherichia coli (E. coli) #8: Water | ChemComp-HOH / | |
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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: 2.51 Å3/Da / Density % sol: 50.92 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→31.4 Å / Num. obs: 44768 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.07 |
Reflection shell | Highest resolution: 2.9 Å / Rmerge(I) obs: 0.408 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1U35 Resolution: 2.9→31.4 Å / Stereochemistry target values: Engh & Huber Details: A 73 chain I and T 74 chain I are linked together. A 217 chain J and T 218 chain J are linked together. However there are T 73A chain I and A 217A chain J present in the structure. The ...Details: A 73 chain I and T 74 chain I are linked together. A 217 chain J and T 218 chain J are linked together. However there are T 73A chain I and A 217A chain J present in the structure. The electron density for this base pair is lost as a result of a convolution between two stretch conformations on the two halves of the nucleosome on either side of the diad axis.
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Refinement step | Cycle: LAST / Resolution: 2.9→31.4 Å
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Refine LS restraints |
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