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- PDB-2hio: HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN -

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Basic information

Entry
Database: PDB / ID: 2hio
TitleHISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN
Components
  • PROTEIN (HISTONE H2A)
  • PROTEIN (HISTONE H2B)
  • PROTEIN (HISTONE H3)
  • PROTEIN (HISTONE H4)
KeywordsSTRUCTURAL 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 / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Interleukin-7 signaling / Chromatin modifying enzymes ...PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Interleukin-7 signaling / Chromatin modifying enzymes / Metalloprotease DUBs / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / UCH proteinases / B-WICH complex positively regulates rRNA expression / Ub-specific processing proteases / Deposition of new CENPA-containing nucleosomes at the centromere / Factors involved in megakaryocyte development and platelet production / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / protein-containing complex binding / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2A-IV / Histone H2B 5 / Histone H2B 7 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsArents, 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
DepositionJun 15, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HISTONE H2A)
B: PROTEIN (HISTONE H2B)
C: PROTEIN (HISTONE H3)
D: PROTEIN (HISTONE H4)


Theoretical massNumber of molelcules
Total (without water)54,5484
Polymers54,5484
Non-polymers00
Water00
1
A: PROTEIN (HISTONE H2A)
B: PROTEIN (HISTONE H2B)
C: PROTEIN (HISTONE H3)
D: PROTEIN (HISTONE H4)

A: PROTEIN (HISTONE H2A)
B: PROTEIN (HISTONE H2B)
C: PROTEIN (HISTONE H3)
D: PROTEIN (HISTONE H4)


Theoretical massNumber of molelcules
Total (without water)109,0968
Polymers109,0968
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area28450 Å2
ΔGint-221 kcal/mol
Surface area30970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.820, 118.820, 102.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN (HISTONE H2A)


Mass: 13838.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02263
#2: Protein PROTEIN (HISTONE H2B)


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 PROTEIN (HISTONE H3)


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 PROTEIN (HISTONE H4)


Mass: 11466.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P62801

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 68 %
Description: THE ENTRY WAS WITHOUT COMPLETE EXPERIMENTAL DETAILS.
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22 M1dropNaCl
31 mMEDTA1drop
410 mMTris-HCl1drop
560 %ammonium sulfate1reservoir
610 mM1reservoirNaP2O7
75 mMEDTA1reservoir
81 %2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceWavelength: 1.5418
DetectorDate: Dec 1, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 13542 / % possible obs: 80 % / Redundancy: 1 %

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementMethod 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
RfactorNum. reflection% reflection
obs0.255 13542 80 %
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 0 0 2850

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