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Yorodumi- PDB-1hio: HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN, ALPHA CARBONS ONLY -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hio | ||||||
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Title | HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN, ALPHA CARBONS ONLY | ||||||
Components |
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Keywords | CHROMOSOMAL PROTEIN / HISTONE / NUCLEOSOME CORE | ||||||
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 / Resolution: 3.1 Å | ||||||
Authors | Arents, G. / Moudrianakis, E.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix. Authors: Arents, G. / Burlingame, R.W. / Wang, B.C. / Love, W.E. / Moudrianakis, E.N. #1: Journal: Biochemistry / Year: 1990 Title: Spectropolarimetric Analysis of the Core Histone Octamer and its Subunits Authors: Godfrey, J.E. / Baxevanis, A.D. / Moudrianakis, E.N. #2: Journal: Science / Year: 1985 Title: Crystallographic Structure of the Octameric Histone Core of the Nucleosome at a Resolution of 3.3 A Authors: Burlingame, R.W. / Love, W.E. / Wang, B.C. / Hamlin, R. / Xuong, N.H. / Moudrianakis, E.N. #3: Journal: Science / Year: 1984 Title: Crystals of the Octameric Histone Core of the Nucleosome Authors: Burlingame, R.W. / Love, W.E. / Moudrianakis, E.N. #4: Journal: Biochemistry / Year: 1980 Title: Reversible Association of Calf Thymus Histones to Form the Symmetrical Octamer (H2Ah2Bh3H4)2: A Case of a Mixed-Associating System Authors: Godfrey, J.E. / Eickbush, T.H. / Moudrianakis, E.N. #5: Journal: Biochemistry / Year: 1978 Title: The Histone Core Complex: An Octamer Assembled by Two Sets of Protein-Protein Interactions Authors: Eickbush, T.H. / Moudrianakis, E.N. #6: Journal: Cell(Cambridge,Mass.) / Year: 1978 Title: The Compaction of DNA Helices Into Either Continuous Supercoils or Folded-Fiber Rods and Toroids Authors: Eickbush, T.H. / Moudrianakis, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hio.cif.gz | 23 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hio.ent.gz | 11.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hio_validation.pdf.gz | 293.1 KB | Display | wwPDB validaton report |
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Full document | 1hio_full_validation.pdf.gz | 293.1 KB | Display | |
Data in XML | 1hio_validation.xml.gz | 730 B | Display | |
Data in CIF | 1hio_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/1hio ftp://data.pdbj.org/pub/pdb/validation_reports/hi/1hio | 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
#1: Protein | Mass: 10401.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: THYMUS / References: UniProt: P02263 |
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#2: Protein | Mass: 9910.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: THYMUS / References: UniProt: P02279, UniProt: P0C1H5*PLUS |
#3: Protein | Mass: 10776.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: THYMUS / References: UniProt: P84229 |
#4: Protein | Mass: 8568.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: THYMUS / References: UniProt: P62801 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.29 Å3/Da / Density % sol: 76.75 % Description: THE ENTRY WAS SUBMITTED IN 1991, WITHOUT COMPLETE EXPERIMENTAL DETAILS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||
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Refinement | Resolution: 3.1→10 Å / σ(F): 2 Details: THIS ENTRY WAS SUBMITTED IN 1991, WITHOUT COMPLETE REFINEMENT DETAILS. PLEASE NOTE THAT THE ORIGINAL COORDINATES SENT TO PDB IN 1991 ARE ALPHA CARBONS ONLY. THE FULL COORDINATES (AS OF ...Details: THIS ENTRY WAS SUBMITTED IN 1991, WITHOUT COMPLETE REFINEMENT DETAILS. PLEASE NOTE THAT THE ORIGINAL COORDINATES SENT TO PDB IN 1991 ARE ALPHA CARBONS ONLY. THE FULL COORDINATES (AS OF 09/15/98) CAN BE FOUND AT THE URL HTTP://WWW.BIO.JHU.EDU/FACULTY/MOUDRIANAKIS/ MOUDRIANAKIS.HTML
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Refinement step | Cycle: LAST / Resolution: 3.1→10 Å
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Refine LS restraints | *PLUS
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