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Yorodumi- PDB-1eqz: X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eqz | ||||||
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Title | X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / NUCLEOSOME / NUCLEOSOME CORE PARTICLE / HISTONE / MICROGRAVITY HISTONE OCTAMER / DNA PALINDROME / DNA PROTEIN COMPLEX / CHROMATIN / CHROMOSOMAL PROTEIN / HISTONE FOLD / BENT DNA / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Condensation of Prophase Chromosomes / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs ...PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Condensation of Prophase Chromosomes / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs / Interleukin-7 signaling / Chromatin modifying enzymes / UCH proteinases / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Ub-specific processing proteases / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / Deposition of new CENPA-containing nucleosomes at the centromere / Factors involved in megakaryocyte development and platelet production / nucleosomal DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / gene expression / protein heterodimerization activity / chromatin binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR, molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Hanson, B.L. / Harp, J.M. / Timm, D.E. / Bunick, G.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Asymmetries in the nucleosome core particle at 2.5 A resolution. Authors: Harp, J.M. / Hanson, B.L. / Timm, D.E. / Bunick, G.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: X-Ray Diffraction Analysis of Crystals Containing Two Fold Symmetric Nucleosome Core Particles Authors: Harp, J.M. / Uberbacher, E.C. / Roberson, A. / Palmer, E. / Gewiess, A. / Bunick, G.J. #2: Journal: Thesis / Year: 1985 Title: Structural Analysis of Members of a Repeated DNA Family in Primates Authors: Hauser, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eqz.cif.gz | 354.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eqz.ent.gz | 272.4 KB | Display | PDB format |
PDBx/mmJSON format | 1eqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eqz_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 1eqz_full_validation.pdf.gz | 498 KB | Display | |
Data in XML | 1eqz_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 1eqz_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eqz ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eqz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 1 types, 2 molecules IJ
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: 146 BP DNA PALINDROME BASED ON 5' HALF OF NUCLEOSOME PHASING SEQUENCE OF ALPHA SATELLITE DNA FROM HUMAN X CHROMOSOME BAM H1 REPEAT |
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-PROTEIN (HISTONE ... , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 13969.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P02263 #3: Protein | Mass: 13953.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P02279, UniProt: P0C1H5*PLUS #4: Protein | Mass: 15421.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P84229 #5: Protein | Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P62801 |
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-Non-polymers , 5 types, 374 molecules
#6: Chemical | ChemComp-K / #7: Chemical | ChemComp-MN / #8: Chemical | #9: Chemical | ChemComp-CAC / | #10: 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: 2.62 Å3/Da / Density % sol: 53.06 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 / Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.003 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.003 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25.4 Å / Num. all: 73319 / Num. obs: 73319 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 42.7 Å2 / Rsym value: 0.053 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 72200 / Num. measured all: 605950 / Rmerge(I) obs: 0.045 |
-Processing
Software |
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Refinement | Method to determine structure: SIR, molecular replacement Starting model: 2HIO, 1AOI Resolution: 2.5→25.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2059998.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.68 Å2 / ksol: 0.393 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→25.34 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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