+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30631 | |||||||||||||||||||||||||||||||||||||||
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Title | The mouse nucleosome structure containing H3mm18 | |||||||||||||||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | complex / chromatin / nucleosome / DNA BINDING PROTEIN / DNA BINDING 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 / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / 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 / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Cleavage of the damaged purine / Metalloprotease DUBs / HDACs deacetylate histones / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / HATs acetylate histones / UCH proteinases / 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 / Estrogen-dependent gene expression / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / nucleosomal DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Hirai S / Takizawa Y | |||||||||||||||||||||||||||||||||||||||
Funding support | Japan, 12 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30631.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-30631-v30.xml emd-30631.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30631_fsc.xml | 6.5 KB | Display | FSC data file |
Images | emd_30631.png | 76.2 KB | ||
Filedesc metadata | emd-30631.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30631 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30631 | HTTPS FTP |
-Validation report
Summary document | emd_30631_validation.pdf.gz | 393.4 KB | Display | EMDB validaton report |
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Full document | emd_30631_full_validation.pdf.gz | 392.9 KB | Display | |
Data in XML | emd_30631_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | emd_30631_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30631 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30631 | HTTPS FTP |
-Related structure data
Related structure data | 7dbhMC 7vbmC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30631.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : The mouse nucleosome containing H3mm18
Entire | Name: The mouse nucleosome containing H3mm18 |
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Components |
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-Supramolecule #1: The mouse nucleosome containing H3mm18
Supramolecule | Name: The mouse nucleosome containing H3mm18 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Histone H3mm18
Macromolecule | Name: Histone H3mm18 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 15.350842 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMARTKQT ARKSTGDKAP RKQLATKAAR KSAPSTGGVK KPHCYRPGTV ALREIRSYQK SSELLIRKLP FQRLVLEIAQ DFKTDLCFQ SAAIGALQEA SEAYLVGLFE DTNLCAIHAK RVTIMPKDTQ LAGYICRECA |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 11.676703 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A type 1-B
Macromolecule | Name: Histone H2A type 1-B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 14.447825 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK UniProtKB: Histone H2A type 1-B |
-Macromolecule #4: Histone H2B type 3-A
Macromolecule | Name: Histone H2B type 3-A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 14.307559 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMPEPSRS TPAPKKGSKK AITKAQKKDG KKRKRGRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIASE ASRLAHYNK RSTITSREVQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSSK UniProtKB: H2B.U histone 2 |
-Macromolecule #5: DNA (126-MER)
Macromolecule | Name: DNA (126-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 44.520383 KDa |
Sequence | 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) ...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) |
-Macromolecule #6: DNA (126-MER)
Macromolecule | Name: DNA (126-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 44.99166 KDa |
Sequence | 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) ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |