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- EMDB-63765: The mouse nucleosome structure containing H3mm15 -

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Basic information

Entry
Database: EMDB / ID: EMD-63765
TitleThe mouse nucleosome structure containing H3mm15
Map dataDeepEMhancer sharpened
Sample
  • Complex: The mouse nucleosome structure containing H3mm15
    • Protein or peptide: H3mm15
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B
    • Protein or peptide: Histone H2B type 3-A
    • DNA: DNA (145-MER)
    • DNA: DNA (145-MER)
KeywordsNucleosome / 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
Histone H2A type 1-B / Histone H4 / H2B.U histone 2
Similarity search - Component
Biological speciesMus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsHo C-H / Kurumizaka H
Funding support Japan, 5 items
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, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63765.png

Downloads & links

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Map

FileDownload / File: emd_63765.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-0.0020417415 - 1.8062856
Average (Standard dev.)0.0033794262 (±0.041421946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63765_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63765_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The mouse nucleosome structure containing H3mm15

EntireName: The mouse nucleosome structure containing H3mm15
Components
  • Complex: The mouse nucleosome structure containing H3mm15
    • Protein or peptide: H3mm15
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B
    • Protein or peptide: Histone H2B type 3-A
    • DNA: DNA (145-MER)
    • DNA: DNA (145-MER)

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Supramolecule #1: The mouse nucleosome structure containing H3mm15

SupramoleculeName: The mouse nucleosome structure containing H3mm15 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: H3mm15

MacromoleculeName: H3mm15 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.462045 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPMARTKQTA RKSTGGKAPR KQLATKAARK SAPSTGGVKK PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQS AAIGALQEAS EAYQVGLFED TNLCAVHAKR VTIMPKDIQL ACRIRGERA

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B

MacromoleculeName: Histone H2A type 1-B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-B

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Macromolecule #4: Histone H2B type 3-A

MacromoleculeName: Histone H2B type 3-A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.307559 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPSRS TPAPKKGSKK AITKAQKKDG KKRKRGRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIASE ASRLAHYNK RSTITSREVQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSSK

UniProtKB: H2B.U histone 2

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Macromolecule #5: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.520383 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG) (DA)(DT)

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Macromolecule #6: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.99166 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DG) (DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1973565
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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