[English] 日本語
Yorodumi
- PDB-1hq3: CRYSTAL STRUCTURE OF THE HISTONE-CORE-OCTAMER IN KCL/PHOSPHATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hq3
TitleCRYSTAL STRUCTURE OF THE HISTONE-CORE-OCTAMER IN KCL/PHOSPHATE
Components
  • HISTONE H2A-IV
  • HISTONE H2B
  • HISTONE H3
  • HISTONE H4-VI
KeywordsDNA BINDING PROTEIN / histone-core octamer / nucleosome / chromatin / structural elements / histone-tail guide helices / tether structures / Cl and Phosphate ions / waters
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
PHOSPHATE ION / Histone H2A-IV / Histone H2B 5 / Histone H2B 7 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChantalat, L. / Nicholson, J.M. / Lambert, S.J. / Reid, A.J. / Donovan, M.J. / Reynolds, C.D. / Wood, C.M. / Baldwin, J.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 A resolution.
Authors: Chantalat, L. / Nicholson, J.M. / Lambert, S.J. / Reid, A.J. / Donovan, M.J. / Reynolds, C.D. / Wood, C.M. / Baldwin, J.P.
History
DepositionDec 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HISTONE H2A-IV
B: HISTONE H2B
C: HISTONE H3
D: HISTONE H4-VI
E: HISTONE H2A-IV
F: HISTONE H2B
G: HISTONE H3
H: HISTONE H4-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,73135
Polymers109,4768
Non-polymers1,25527
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33990 Å2
ΔGint-461 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.560, 158.560, 102.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein HISTONE H2A-IV /


Mass: 13969.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: EXTRACTED AS PART OF OCTAMER IN KCL/PHOSPHATE / Source: (natural) Gallus gallus (chicken) / Organelle: CHICK-ERYTHROCYTE NUCLEI / References: UniProt: P02263
#2: Protein HISTONE H2B /


Mass: 13953.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: EXTRACTED AS PART OF OCTAMER IN KCL/PHOSPHATE / Source: (natural) Gallus gallus (chicken) / Organelle: CHICK-ERYTHROCYTE NUCLEI / References: UniProt: P02279, UniProt: P0C1H5*PLUS
#3: Protein HISTONE H3 /


Mass: 15421.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: EXTRACTED AS PART OF OCTAMER IN KCL/PHOSPHATE / Source: (natural) Gallus gallus (chicken) / Organelle: CHICK-ERYTHROCYTE NUCLEI / References: UniProt: P84229
#4: Protein HISTONE H4-VI /


Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: EXTRACTED AS PART OF OCTAMER IN KCL/PHOSPHATE / Source: (natural) Gallus gallus (chicken) / Organelle: CHICK-ERYTHROCYTE NUCLEI / References: UniProt: P62801

-
Non-polymers , 3 types, 464 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growMethod: microdialysis / pH: 6.7
Details: 2.0M KCL, 1.35M phosphate, pH 6.6, pH 6.7, MICRODIALYSIS
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.475 M11K2HPO4
20.475 M11KH2PO4
320 mg/mlprotein11
42 M12KCl
50.675 M12K2HPO4
60.675 M12KH2PO4

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX7.211.488
SYNCHROTRONSRS PX9.52
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEMar 1, 1997plane
MARRESEARCH2CCDSep 1, 1998torroidal mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ge 111SINGLE WAVELENGTHMx-ray1
2Si 111 channelSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 74806 / Num. obs: 74806 / % possible obs: 97.4 % / Redundancy: 2.26 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.331 / % possible all: 97.1
Reflection
*PLUS
Num. measured all: 169058
Reflection shell
*PLUS
% possible obs: 97.1 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: histone octamer PDB entry 1HIO

1hio


Resolution: 2.15→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 4451 6 %Random
Rwork0.2144 ---
all-74806 --
obs-74806 97.4 %-
Solvent computationSolvent model: flat model / Bsol: 61.1947 Å2 / ksol: 0.371738 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 47 437 6469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it2.391.5
X-RAY DIFFRACTIONc_mcangle_it3.632
X-RAY DIFFRACTIONc_scbond_it4.022
X-RAY DIFFRACTIONc_scangle_it5.72.5
LS refinement shellResolution: 2.15→2.28 Å / Total num. of bins used: 6 / % reflection obs: 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 6 % / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
X-RAY DIFFRACTIONc_mcbond_it2.391.5
X-RAY DIFFRACTIONc_scbond_it4.022
X-RAY DIFFRACTIONc_mcangle_it3.632
X-RAY DIFFRACTIONc_scangle_it5.72.5

+
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