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Open data
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Basic information
Entry | Database: PDB / ID: 6k1i | ||||||
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Title | Human nucleosome core particle with gammaH2A.X variant | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Nucleosome / gammaH2A.X / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() chromatin-protein adaptor activity / XY body / protein localization to site of double-strand break / response to ionizing radiation / site of DNA damage / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus ...chromatin-protein adaptor activity / XY body / protein localization to site of double-strand break / response to ionizing radiation / site of DNA damage / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / positive regulation of DNA repair / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / condensed nuclear chromosome / innate immune response in mucosa / DNA damage checkpoint signaling / meiotic cell cycle / PRC2 methylates histones and DNA / replication fork / male germ cell nucleus / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / cellular response to gamma radiation / PKMTs methylate histone lysines / cerebral cortex development / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / cellular senescence / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / double-strand break repair / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / site of double-strand break / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / antibacterial humoral response / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / damaged DNA binding / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / nuclear speck / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / centrosome / DNA damage response / enzyme binding / protein-containing complex Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, D. / De Falco, L. / Davey, C.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome. Authors: Sharma, D. / De Falco, L. / Padavattan, S. / Rao, C. / Geifman-Shochat, S. / Liu, C.F. / Davey, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 330.8 KB | Display | ![]() |
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PDB format | ![]() | 250.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15719.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ Production host: ![]() ![]() #2: Protein | Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 Production host: ![]() ![]() #3: Protein | Mass: 15454.880 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Serine at position 144 is chemically phosphorylated (actual position S139) Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 14217.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45193.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#6: DNA chain | Mass: 45554.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 57 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Chemical | ChemComp-MN / #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.64 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: potassium chloride, manganese chloride, potassium cacodylate PH range: 6 |
-Data collection
Diffraction | Mean temperature: 98.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→93.7 Å / Num. obs: 54043 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 95.485 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.059 / Rrim(I) all: 0.202 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 11.3 % / Num. unique obs: 7776 / Rpim(I) all: 0.779 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.93 Å2 / Biso mean: 87.721 Å2 / Biso min: 32.82 Å2
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Refinement step | Cycle: final / Resolution: 2.75→93.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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