[English] 日本語
Yorodumi
- PDB-2hio: HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN -

+
Open data


ID or keywords:

Loading...

-
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 / Metalloprotease DUBs / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...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 / Metalloprotease DUBs / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Interleukin-7 signaling / Chromatin modifying enzymes / HATs acetylate histones / Ub-specific processing proteases / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / 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 / nucleosome assembly / structural constituent of chromatin / nucleosome / protein heterodimerization activity / protein-containing complex binding / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / 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, subunit A / Histone, subunit A / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more