7VBM

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant.

Hirai, S.Tomimatsu, K.Miyawaki-Kuwakado, A.Takizawa, Y.Komatsu, T.Tachibana, T.Fukushima, Y.Takeda, Y.Negishi, L.Kujirai, T.Koyama, M.Ohkawa, Y.Kurumizaka, H.

(2022) Nucleic Acids Res 50: 72-91

  • DOI: 10.1093/nar/gkab1137
  • Primary Citation of Related Structures:  
    7DBH, 7VBM

  • PubMed 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 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 ...

    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.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3mm18A, E139Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F106Mus musculusMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62806 (Mus musculus)
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Go to UniProtKB:  P62806
IMPC:  MGI:2448443
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UniProt GroupP62806
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-BC, G133Mus musculusMutation(s): 0 
Gene Names: Hist1h2abH2ac4
UniProt
Find proteins for C0HKE1 (Mus musculus)
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UniProt GroupC0HKE1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 3-AD, H129Mus musculusMutation(s): 0 
Gene Names: Hist3h2ba
UniProt
Find proteins for Q9D2U9 (Mus musculus)
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UniProt GroupQ9D2U9
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (126-MER)I 145Mus musculus
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Entity ID: 6
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DNA (126-MER)J 145Mus musculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR16G1
Japan Society for the Promotion of Science (JSPS)JapanJP18H05534
Japan Society for the Promotion of Science (JSPS)JapanJP18K14677
Japan Society for the Promotion of Science (JSPS)JapanJP18H05527
Japan Society for the Promotion of Science (JSPS)JapanJP19H05244
Japan Society for the Promotion of Science (JSPS)JapanJP19K06522
Japan Society for the Promotion of Science (JSPS)JapanJP20H00456
Japan Society for the Promotion of Science (JSPS)JapanJP20H04846
Japan Society for the Promotion of Science (JSPS)JapanJP20H00449
Japan Science and TechnologyJapanJPMJER1901
Japan Society for the Promotion of Science (JSPS)JapanJP20K15711
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101076

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references