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- EMDB-31882: The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv -

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Basic information

Entry
Database: EMDB / ID: EMD-31882
TitleThe mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv
Map dataNucleosome containing H3mm18 aided by PL2-6 scFv
Sample
  • Complex: The mouse nucleosome containing H3mm18 aided by PL2-6 scFv
    • Protein or peptide: Histone H3mm18
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B
    • Protein or peptide: Histone H2B type 3-A
    • DNA: DNA (126-MER)
    • DNA: DNA (126-MER)
Function / homology
Function and homology information


Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / SUMOylation of chromatin organization proteins / SIRT1 negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint ...Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / SUMOylation of chromatin organization proteins / SIRT1 negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / RNA Polymerase I Promoter Opening / HDMs demethylate histones / Processing of DNA double-strand break ends / Transcriptional regulation by small RNAs / Metalloprotease DUBs / B-WICH complex positively regulates rRNA expression / Nonhomologous End-Joining (NHEJ) / HDACs deacetylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / UCH proteinases / PRC2 methylates histones and DNA / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / Oxidative Stress Induced Senescence / Ub-specific processing proteases / negative regulation of megakaryocyte differentiation / DNA replication-independent chromatin assembly / DNA replication-dependent chromatin assembly / heterochromatin assembly / nuclear chromosome / nucleosome assembly / nucleosome / DNA-templated transcription, initiation / protein heterodimerization activity / protein domain specific binding / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site ...Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / 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 / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHirai S / Takizawa Y / Kujirai T / Kurumizaka H
Funding support Japan, 12 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP18K14677 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05527 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05244 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00456 Japan
Japan Society for the Promotion of Science (JSPS)JP20H04846 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15711 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101076 Japan
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant.
Authors: Seiya Hirai / Kosuke Tomimatsu / Atsuko Miyawaki-Kuwakado / Yoshimasa Takizawa / Tetsuro Komatsu / Taro Tachibana / Yutaro Fukushima / Yasuko Takeda / Lumi Negishi / Tomoya Kujirai / Masako ...Authors: Seiya Hirai / Kosuke Tomimatsu / Atsuko Miyawaki-Kuwakado / Yoshimasa Takizawa / Tetsuro Komatsu / Taro Tachibana / Yutaro Fukushima / Yasuko Takeda / Lumi Negishi / Tomoya Kujirai / Masako Koyama / Yasuyuki Ohkawa / Hitoshi Kurumizaka /
Abstract: Histone H3mm18 is a non-allelic H3 variant expressed in skeletal muscle and brain in mice. However, its function has remained enigmatic. We found that H3mm18 is incorporated into chromatin in cells ...Histone H3mm18 is a non-allelic H3 variant expressed in skeletal muscle and brain in mice. However, its function has remained enigmatic. We found that H3mm18 is incorporated into chromatin in cells with low efficiency, as compared to H3.3. We determined the structures of the nucleosome core particle (NCP) containing H3mm18 by cryo-electron microscopy, which revealed that the entry/exit DNA regions are drastically disordered in the H3mm18 NCP. Consistently, the H3mm18 NCP is substantially unstable in vitro. The forced expression of H3mm18 in mouse myoblast C2C12 cells markedly suppressed muscle differentiation. A transcriptome analysis revealed that the forced expression of H3mm18 affected the expression of multiple genes, and suppressed a group of genes involved in muscle development. These results suggest a novel gene expression regulation system in which the chromatin landscape is altered by the formation of unusual nucleosomes with a histone variant, H3mm18, and provide important insight into understanding transcription regulation by chromatin.
History
DepositionAug 31, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vbm
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31882.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNucleosome containing H3mm18 aided by PL2-6 scFv
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
Contour LevelBy AUTHOR: 2.75 / Movie #1: 3.5
Minimum - Maximum-18.142206 - 31.733114
Average (Standard dev.)-2.4778333e-09 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-18.14231.733-0.000

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Supplemental data

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Sample components

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Entire : The mouse nucleosome containing H3mm18 aided by PL2-6 scFv

EntireName: The mouse nucleosome containing H3mm18 aided by PL2-6 scFv
Components
  • Complex: The mouse nucleosome containing H3mm18 aided by PL2-6 scFv
    • Protein or peptide: Histone H3mm18
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B
    • Protein or peptide: Histone H2B type 3-A
    • DNA: DNA (126-MER)
    • DNA: DNA (126-MER)

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Supramolecule #1: The mouse nucleosome containing H3mm18 aided by PL2-6 scFv

SupramoleculeName: The mouse nucleosome containing H3mm18 aided by PL2-6 scFv
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Histone H3mm18

MacromoleculeName: Histone H3mm18 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.350842 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGDKAP RKQLATKAAR KSAPSTGGVK KPHCYRPGTV ALREIRSYQK SSELLIRKLP FQRLVLEIAQ DFKTDLCFQ SAAIGALQEA SEAYLVGLFE DTNLCAIHAK RVTIMPKDTQ LAGYICRECA

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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

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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

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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

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Macromolecule #5: DNA (126-MER)

MacromoleculeName: DNA (126-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
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 (126-MER)

MacromoleculeName: DNA (126-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
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-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224465
FSC plot (resolution estimation)

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