[English] 日本語
Yorodumi
- PDB-1eqz: X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eqz
TitleX-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION
Components
  • (PROTEIN (HISTONE ...) x 4
  • 146 NUCLEOTIDES LONG DNA
KeywordsSTRUCTURAL PROTEIN/DNA / NUCLEOSOME / NUCLEOSOME CORE PARTICLE / HISTONE / MICROGRAVITY HISTONE OCTAMER / DNA PALINDROME / DNA PROTEIN COMPLEX / CHROMATIN / CHROMOSOMAL PROTEIN / HISTONE FOLD / BENT DNA / STRUCTURAL PROTEIN-DNA COMPLEX
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
CACODYLATE ION / : / : / DNA / DNA (> 10) / DNA (> 100) / 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 / SIR, molecular replacement / Resolution: 2.5 Å
AuthorsHanson, B.L. / Harp, J.M. / Timm, D.E. / Bunick, G.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Asymmetries in the nucleosome core particle at 2.5 A resolution.
Authors: Harp, J.M. / Hanson, B.L. / Timm, D.E. / Bunick, G.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: X-Ray Diffraction Analysis of Crystals Containing Two Fold Symmetric Nucleosome Core Particles
Authors: Harp, J.M. / Uberbacher, E.C. / Roberson, A. / Palmer, E. / Gewiess, A. / Bunick, G.J.
#2: Journal: Thesis / Year: 1985
Title: Structural Analysis of Members of a Repeated DNA Family in Primates
Authors: Hauser, L.J.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
I: 146 NUCLEOTIDES LONG DNA
J: 146 NUCLEOTIDES LONG DNA
A: PROTEIN (HISTONE H2A)
B: PROTEIN (HISTONE H2B)
C: PROTEIN (HISTONE H3)
D: PROTEIN (HISTONE H4)
E: PROTEIN (HISTONE H2A)
F: PROTEIN (HISTONE H2B)
G: PROTEIN (HISTONE H3)
H: PROTEIN (HISTONE H4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,89235
Polymers199,58610
Non-polymers1,30625
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.280, 109.710, 181.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

-
DNA chain , 1 types, 2 molecules IJ

#1: DNA chain 146 NUCLEOTIDES LONG DNA


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 146 BP DNA PALINDROME BASED ON 5' HALF OF NUCLEOSOME PHASING SEQUENCE OF ALPHA SATELLITE DNA FROM HUMAN X CHROMOSOME BAM H1 REPEAT

-
PROTEIN (HISTONE ... , 4 types, 8 molecules AEBFCGDH

#2: Protein PROTEIN (HISTONE H2A)


Mass: 13969.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P02263
#3: Protein PROTEIN (HISTONE H2B)


Mass: 13953.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P02279, UniProt: P0C1H5*PLUS
#4: Protein PROTEIN (HISTONE H3)


Mass: 15421.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P84229
#5: Protein PROTEIN (HISTONE H4)


Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER / Source: (natural) Gallus gallus (chicken) / Organelle: ERYTHROCYTE NUCLEUS / Tissue: BLOOD / References: UniProt: P62801

-
Non-polymers , 5 types, 374 molecules

#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6 / Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM11KCl
210 mMpotassium cacodylate11
31 mMPMSF11
550 mM12KCl
610 mMpotassium cacodylate12
71 mMPMSF12
411MnCl2high concentration
812MnCl2low concentration

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.003
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.5→25.4 Å / Num. all: 73319 / Num. obs: 73319 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 42.7 Å2 / Rsym value: 0.053
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 72200 / Num. measured all: 605950 / Rmerge(I) obs: 0.045

-
Processing

Software
NameClassification
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
CNSphasing
RefinementMethod to determine structure: SIR, molecular replacement
Starting model: 2HIO, 1AOI

2hio

1aoi


Resolution: 2.5→25.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2059998.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 7303 10.1 %RANDOM
Rwork0.219 ---
obs0.219 72200 98.6 %-
all-72200 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.68 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.98 Å20 Å20 Å2
2---5.53 Å20 Å2
3----0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-25.4 Å
Luzzati sigma a0.29 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.5→25.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 5988 29 349 13272
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.641.5
X-RAY DIFFRACTIONc_mcangle_it4.962
X-RAY DIFFRACTIONc_scbond_it4.682
X-RAY DIFFRACTIONc_scangle_it5.982.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33

+
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