+Open data
-Basic information
Entry | Database: PDB / ID: 2hio | ||||||
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Title | HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / DNA BINDING PROTEIN / HISTONE / CHROMOSOMAL PROTEIN | ||||||
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 / MOLECULAR REPLACEMENT / 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 | 2hio.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hio.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/2hio ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2hio | HTTPS FTP |
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-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: 13838.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02263 |
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#2: Protein | Mass: 13822.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02279, UniProt: P0C1H5*PLUS |
#3: Protein | Mass: 15421.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P84229 |
#4: Protein | Mass: 11466.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P62801 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 68 % Description: THE ENTRY WAS WITHOUT COMPLETE EXPERIMENTAL DETAILS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Date: Dec 1, 1991 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 13542 / % possible obs: 80 % / Redundancy: 1 % |
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→10 Å / σ(F): 2 Details: CHICKEN ERYTHROCYTE CORE HISTONE OCTAMER AT 3.1 A RESOLUTIO (ARENTS ET AL., 1991). IN THE SET LISTED BELOW B VALUES HA BEEN ARBITRARILY SET AND DO NOT REPRESENT THE CURRENT STATE REFINEMENT. ...Details: CHICKEN ERYTHROCYTE CORE HISTONE OCTAMER AT 3.1 A RESOLUTIO (ARENTS ET AL., 1991). IN THE SET LISTED BELOW B VALUES HA BEEN ARBITRARILY SET AND DO NOT REPRESENT THE CURRENT STATE REFINEMENT. CHAIN IDENTIFIERS H2A(1) = A H2B(1) = B H3(1) = C H4(1) = D
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Refinement step | Cycle: LAST / Resolution: 3.1→10 Å
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