+Open data
-Basic information
Entry | Database: PDB / ID: 6hkt | ||||||
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Title | Structure of an H1-bound 6-nucleosome array | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / chromatin / nucleosome array / chromatin fiber | ||||||
Function / homology | Function and homology information 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 / epigenetic regulation of gene expression / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...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 / epigenetic regulation of gene expression / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / gene expression / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 9.7 Å | ||||||
Authors | Garcia-Saez, I. / Dimitrov, S. / Petosa, C. | ||||||
Funding support | France, 1items
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Citation | Journal: Mol. Cell / Year: 2018 Title: Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation. Authors: Garcia-Saez, I. / Menoni, H. / Boopathi, R. / Shukla, M.S. / Soueidan, L. / Noirclerc-Savoye, M. / Le Roy, A. / Skoufias, D.A. / Bednar, J. / Hamiche, A. / Angelov, D. / Petosa, C. / Dimitrov, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hkt.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6hkt.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6hkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/6hkt ftp://data.pdbj.org/pub/pdb/validation_reports/hk/6hkt | HTTPS FTP |
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-Related structure data
Related structure data | 3lz0S 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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-Components
-Protein , 4 types, 48 molecules AEaeKOkoUYuyBFbfLPlpVZvzCGcgMQ...
#1: Protein | Mass: 15719.445 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG Source: (gene. exp.) Homo sapiens (human) Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68431 #2: Protein | Mass: 11676.703 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG Source: (gene. exp.) Homo sapiens (human) 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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62805 #3: Protein | Mass: 14447.825 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04908 #4: Protein | Mass: 14217.516 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06899 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 344755.281 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Six tandem 187-bp repeats containing Widom 601 sequence Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 348512.312 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Six tandem 187-bp repeats containing Widom 601 sequence Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.42 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 9.7→49.1 Å / Num. obs: 11252 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.09 / Rrim(I) all: 0.23 / Net I/σ(I): 7 |
Reflection shell | Resolution: 9.7→10.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3152 / CC1/2: 0.604 / Rpim(I) all: 0.362 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LZ0 Resolution: 9.7→49.074 Å / SU ML: 1.68 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 34.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 9.7→49.074 Å
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Refine LS restraints |
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LS refinement shell |
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