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- PDB-7vbm: The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vbm | |||||||||||||||||||||||||||||||||||||||
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Title | The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv | |||||||||||||||||||||||||||||||||||||||
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![]() | DNA BINDING PROTEIN / complex / chromatin / nucleosome / DNA BINDING PROTEIN-DNA complex | |||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / DNA Damage/Telomere Stress Induced Senescence / SUMOylation of chromatin organization proteins / Recognition and association of DNA glycosylase with site containing an affected purine / G2/M DNA damage checkpoint / Cleavage of the damaged purine / HDMs demethylate histones / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes ...Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / DNA Damage/Telomere Stress Induced Senescence / SUMOylation of chromatin organization proteins / Recognition and association of DNA glycosylase with site containing an affected purine / G2/M DNA damage checkpoint / Cleavage of the damaged purine / HDMs demethylate histones / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes / HDACs deacetylate histones / Metalloprotease DUBs / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / UCH proteinases / 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 / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / heterochromatin organization / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||||||||||||||||||||||||||
![]() | Hirai, S. / Takizawa, Y. / Kujirai, T. / Kurumizaka, H. | |||||||||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.2 KB | Display | ![]() |
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PDB format | ![]() | 186 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 821.3 KB | Display | ![]() |
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Full document | ![]() | 830.1 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 48 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31882MC ![]() 7dbhC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15350.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4 Production host: ![]() ![]() #3: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 14307.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44520.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#6: DNA chain | Mass: 44991.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: The mouse nucleosome containing H3mm18 aided by PL2-6 scFv Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 58.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224465 / Symmetry type: POINT |