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- PDB-9mb2: The mouse nucleosome structure containing H3mm15 -

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Basic information

Entry
Database: PDB / ID: 9mb2
TitleThe mouse nucleosome structure containing H3mm15
Components
  • (DNA (145-MER)) x 2
  • H3mm15
  • Histone H2A type 1-B
  • Histone H2B type 3-A
  • Histone H4
KeywordsNUCLEAR PROTEIN/DNA / Nucleosome / Nucleoprotein / Histone-DNA complex / NUCLEAR PROTEIN / NUCLEAR 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 / Regulation of PD-L1(CD274) transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / HDMs demethylate histones / Nonhomologous End-Joining (NHEJ) ...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 / Regulation of PD-L1(CD274) transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / HDMs demethylate histones / Nonhomologous End-Joining (NHEJ) / Negative Regulation of CDH1 Gene Transcription / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / PRC2 methylates histones and DNA / HATs acetylate histones / Metalloprotease DUBs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PKMTs methylate histone lysines / UCH proteinases / Processing of DNA double-strand break ends / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RMTs methylate histone arginines / Estrogen-dependent gene expression / CENP-A containing nucleosome / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / innate immune response in mucosa / structural constituent of chromatin / nucleosome / nucleosome assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / antibacterial humoral response / chromatin organization / protein heterodimerization activity / protein-containing complex / : / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
: / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2A conserved site / Histone H2A signature. / Histone H2B 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 H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B / Histone H4 / H2B.U histone 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsHo, C.-H. / Kurumizaka, H.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR24T3 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121009 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
CitationJournal: To Be Published
Title: Histone H3.3 subvariant H3mm15 is required for normal spermatogenesis by regulating gene expression
Authors: Wu, Q. / Harada, A. / Ho, C.-H. / Tanaka, K. / Maehara, K. / Shimada, R. / Ishiguro, K. / Oki, S. / Kurumizaka, H. / Takemoto, T. / Ohkawa, Y.
History
DepositionMar 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H3mm15
B: Histone H4
C: Histone H2A type 1-B
D: Histone H2B type 3-A
E: H3mm15
F: Histone H4
G: Histone H2A type 1-B
H: Histone H2B type 3-A
I: DNA (145-MER)
J: DNA (145-MER)


Theoretical massNumber of molelcules
Total (without water)201,30010
Polymers201,30010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein H3mm15


Mass: 15462.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#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 (E. coli) / 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 / Production host: Escherichia coli (E. coli) / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D2U9

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The mouse nucleosome structure containing H3mm15 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2250 nm / Nominal defocus min: 1250 nm
Image recordingElectron dose: 60.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1973565 / Symmetry type: POINT
RefinementHighest resolution: 2.39 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512718
ELECTRON MICROSCOPYf_angle_d0.56918420
ELECTRON MICROSCOPYf_dihedral_angle_d30.8163752
ELECTRON MICROSCOPYf_chiral_restr0.0372096
ELECTRON MICROSCOPYf_plane_restr0.0041328

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