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- PDB-1hio: HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN, ALPHA CARBONS ONLY -

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Basic information

Entry
Database: PDB / ID: 1hio
TitleHISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN, ALPHA CARBONS ONLY
Components
  • HISTONE H2A
  • HISTONE H2B
  • HISTONE H3
  • HISTONE H4
KeywordsCHROMOSOMAL 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 / 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 H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A ...: / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / Histone-fold
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 / 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
DepositionSep 19, 1991Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,6564
Polymers39,6564
Non-polymers00
Water00
1
A: HISTONE H2A
B: HISTONE H2B
C: HISTONE H3
D: HISTONE H4

A: HISTONE H2A
B: HISTONE H2B
C: HISTONE H3
D: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)79,3128
Polymers79,3128
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
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 HISTONE H2A / Coordinate model: Cα atoms only


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
#2: Protein HISTONE H2B / Coordinate model: Cα atoms only


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 HISTONE H3 / Coordinate model: Cα atoms only


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 HISTONE H4 / Coordinate model: Cα atoms only


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.29 Å3/Da / Density % sol: 76.75 %
Description: THE ENTRY WAS SUBMITTED IN 1991, WITHOUT COMPLETE EXPERIMENTAL DETAILS.
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 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
RfactorNum. reflection
obs0.255 13542
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms354 0 0 0 354
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.039

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