[English] 日本語
Yorodumi
- PDB-5xm0: The mouse nucleosome structure containing H2A, H2B type3-A, H3.3,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xm0
TitleThe mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4
Components
  • DNA (146-MER)
  • Histone H2A type 1-B
  • Histone H2B type 3-A
  • Histone H3.3
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / chromatin / DNA-Protein complex / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs ...Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / HDACs deacetylate histones / PRC2 methylates histones and DNA / UCH proteinases / Processing of DNA double-strand break ends / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / negative regulation of chromosome condensation / Barr body / : / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / pericentric heterochromatin formation / inner kinetochore / Ub-specific processing proteases / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / oogenesis / nucleus organization / chromosome, centromeric region / spermatid development / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / embryo implantation / multicellular organism growth / male gonad development / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / chromatin organization / positive regulation of cell growth / spermatogenesis / chromosome, telomeric region / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin / 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
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B / Histone H4 / Histone H3.3 / H2B.U histone 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.874 Å
AuthorsTaguchi, H. / Horikoshi, N. / Kurumizaka, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
Ministry of Education, Culture, Sports, Science and Technology25116002 Japan
the Japan Agency for Medical Research and Development Japan
CitationJournal: Nat Commun / Year: 2018
Title: Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration.
Authors: Harada, A. / Maehara, K. / Ono, Y. / Taguchi, H. / Yoshioka, K. / Kitajima, Y. / Xie, Y. / Sato, Y. / Iwasaki, T. / Nogami, J. / Okada, S. / Komatsu, T. / Semba, Y. / Takemoto, T. / Kimura, ...Authors: Harada, A. / Maehara, K. / Ono, Y. / Taguchi, H. / Yoshioka, K. / Kitajima, Y. / Xie, Y. / Sato, Y. / Iwasaki, T. / Nogami, J. / Okada, S. / Komatsu, T. / Semba, Y. / Takemoto, T. / Kimura, H. / Kurumizaka, H. / Ohkawa, Y.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
C: Histone H2A type 1-B
D: Histone H2B type 3-A
E: Histone H3.3
F: Histone H4
G: Histone H2A type 1-B
H: Histone H2B type 3-A
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)202,25810
Polymers202,25810
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55590 Å2
ΔGint-398 kcal/mol
Surface area73030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.523, 110.095, 182.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resseq 16:70 or resseq 72:117))
21(chain G and (resseq 16:70 or resseq 72:117))
12(chain B and (resseq 25:34 or resseq 36:101))
22(chain F and (resseq 25:34 or resseq 36:101))
13(chain A and (resseq 38:52 or resseq 54:134))
23(chain E and (resseq 38:52 or resseq 54:134))
14(chain D and (resseq 35:85 or resseq 87:102 or (resid...
24(chain H and (resseq 35:85 or resseq 87:102 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRALAALA(chain C and (resseq 16:70 or resseq 72:117))CC16 - 7020 - 74
121ASPASPPROPRO(chain C and (resseq 16:70 or resseq 72:117))CC72 - 11776 - 121
211THRTHRALAALA(chain G and (resseq 16:70 or resseq 72:117))GG16 - 7020 - 74
221ASPASPPROPRO(chain G and (resseq 16:70 or resseq 72:117))GG72 - 11776 - 121
112ASNASNILEILE(chain B and (resseq 25:34 or resseq 36:101))BB25 - 3429 - 38
122ARGARGGLYGLY(chain B and (resseq 25:34 or resseq 36:101))BB36 - 10140 - 105
212ASNASNILEILE(chain F and (resseq 25:34 or resseq 36:101))FF25 - 3429 - 38
222ARGARGGLYGLY(chain F and (resseq 25:34 or resseq 36:101))FF36 - 10140 - 105
113PROPROARGARG(chain A and (resseq 38:52 or resseq 54:134))AA38 - 5242 - 56
123TYRTYRARGARG(chain A and (resseq 38:52 or resseq 54:134))AA54 - 13458 - 138
213PROPROARGARG(chain E and (resseq 38:52 or resseq 54:134))EE38 - 5242 - 56
223TYRTYRARGARG(chain E and (resseq 38:52 or resseq 54:134))EE54 - 13458 - 138
114GLUGLULYSLYS(chain D and (resseq 35:85 or resseq 87:102 or (resid...DD35 - 8539 - 89
124SERSERLEULEU(chain D and (resseq 35:85 or resseq 87:102 or (resid...DD87 - 10291 - 106
134PROPROPROPRO(chain D and (resseq 35:85 or resseq 87:102 or (resid...DD103107
144ARGARGSERSER(chain D and (resseq 35:85 or resseq 87:102 or (resid...DD31 - 12435 - 128
154ARGARGSERSER(chain D and (resseq 35:85 or resseq 87:102 or (resid...DD31 - 12435 - 128
164ARGARGSERSER(chain D and (resseq 35:85 or resseq 87:102 or (resid...DD31 - 12435 - 128
174ARGARGSERSER(chain D and (resseq 35:85 or resseq 87:102 or (resid...DD31 - 12435 - 128
184ARGARGSERSER(chain D and (resseq 35:85 or resseq 87:102 or (resid...DD31 - 12435 - 128
214GLUGLULYSLYS(chain H and (resseq 35:85 or resseq 87:102 or (resid...HH35 - 8539 - 89
224SERSERLEULEU(chain H and (resseq 35:85 or resseq 87:102 or (resid...HH87 - 10291 - 106
234PROPROPROPRO(chain H and (resseq 35:85 or resseq 87:102 or (resid...HH103107
244ARGARGSERSER(chain H and (resseq 35:85 or resseq 87:102 or (resid...HH33 - 12437 - 128
254ARGARGSERSER(chain H and (resseq 35:85 or resseq 87:102 or (resid...HH33 - 12437 - 128
264ARGARGSERSER(chain H and (resseq 35:85 or resseq 87:102 or (resid...HH33 - 12437 - 128
274ARGARGSERSER(chain H and (resseq 35:85 or resseq 87:102 or (resid...HH33 - 12437 - 128
284ARGARGSERSER(chain H and (resseq 35:85 or resseq 87:102 or (resid...HH33 - 12437 - 128

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.3


Mass: 15643.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H3f3a, H3.3a, H3f3b, H3.3b / Plasmid: pH3.3 / Production host: Escherichia coli BL21(DE3) / Strain (production host): BL21(DE3) / References: UniProt: P84244
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4
Production host: Escherichia coli / Strain (production host): JM109(DE3) / References: UniProt: P62806
#3: Protein Histone H2A type 1-B


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist1h2ab / Plasmid: pH2A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C0HKE1
#4: Protein Histone H2B type 3-A


Mass: 14307.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist3h2ba / Plasmid: pH2B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9D2U9

-
DNA chain / Non-polymers , 2 types, 14 molecules IJ

#5: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEM-T(easy) / Production host: Escherichia coli DH5alpha (bacteria) / Strain (production host): DH5alpha
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: potassium cacodylate, potassium chloride, manganese chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 49349 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 57.79 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.045 / Rrim(I) all: 0.094 / Χ2: 1.734 / Net I/σ(I): 11.6 / Num. measured all: 203874
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.87-2.974.20.548880.8030.2780.5741.554100
2.97-3.094.20.36848510.8770.2050.4231.62699.9
3.09-3.234.20.25149110.9410.1390.2881.637100
3.23-3.44.20.17748910.9670.0990.2041.72599.9
3.4-3.624.20.12148950.9860.0670.1391.765100
3.62-3.894.20.0949200.9920.0490.1031.75699.9
3.89-4.294.10.06849280.9940.0380.0781.80199.8
4.29-4.914.10.05349580.9960.0290.061.70899.7
4.91-6.184.10.0549880.9970.0270.0571.75599.4
6.18-503.90.03751190.9980.0210.0432.0297.6

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000704wdata scaling
PHASER2.5.1phasing
PDB_EXTRACT3.22data extraction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AV2

3av2


Resolution: 2.874→48.904 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.08 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2553 2494 5.06 %
Rwork0.2189 46794 -
obs0.2208 49288 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.93 Å2 / Biso mean: 71.2038 Å2 / Biso min: 19.17 Å2
Refinement stepCycle: final / Resolution: 2.874→48.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5958 5980 0 12 11950
Biso mean---41.32 -
Num. residues----1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112746
X-RAY DIFFRACTIONf_angle_d1.19418465
X-RAY DIFFRACTIONf_chiral_restr0.0592098
X-RAY DIFFRACTIONf_plane_restr0.0081327
X-RAY DIFFRACTIONf_dihedral_angle_d26.0386653
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C928X-RAY DIFFRACTION12.27TORSIONAL
12G928X-RAY DIFFRACTION12.27TORSIONAL
21B720X-RAY DIFFRACTION12.27TORSIONAL
22F720X-RAY DIFFRACTION12.27TORSIONAL
31A909X-RAY DIFFRACTION12.27TORSIONAL
32E909X-RAY DIFFRACTION12.27TORSIONAL
41D778X-RAY DIFFRACTION12.27TORSIONAL
42H778X-RAY DIFFRACTION12.27TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8741-2.92940.36141460.31452503264998
2.9294-2.98910.33651390.295625902729100
2.9891-3.05410.27611480.263425662714100
3.0541-3.12520.31361570.259725452702100
3.1252-3.20330.28611220.269725902712100
3.2033-3.28990.33481320.264325702702100
3.2899-3.38670.29431380.24625872725100
3.3867-3.4960.2631460.225525992745100
3.496-3.62090.24661290.211525862715100
3.6209-3.76580.26081310.212126142745100
3.7658-3.93710.27571260.21926212747100
3.9371-4.14460.2471400.206525912731100
4.1446-4.40410.22741170.194626292746100
4.4041-4.74390.22791260.195326112737100
4.7439-5.22080.24711340.199126272761100
5.2208-5.97510.26021470.22442621276899
5.9751-7.52360.27281590.22632647280699
7.5236-48.91070.18581570.18252697285496

+
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