6L4A

H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.3 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

Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome.

Takizawa, Y.Ho, C.H.Tachiwana, H.Matsunami, H.Kobayashi, W.Suzuki, M.Arimura, Y.Hori, T.Fukagawa, T.Ohi, M.D.Wolf, M.Kurumizaka, H.

(2020) Structure 28: 44

  • DOI: 10.1016/j.str.2019.10.016
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The histone H3 variant CENP-A is a crucial epigenetic marker for centromere specification. CENP-A forms a characteristic nucleosome and dictates the higher-order configuration of centromeric chromatin. However, little is known about how the CENP-A nu ...

    The histone H3 variant CENP-A is a crucial epigenetic marker for centromere specification. CENP-A forms a characteristic nucleosome and dictates the higher-order configuration of centromeric chromatin. However, little is known about how the CENP-A nucleosome affects the architecture of centromeric chromatin. In this study, we reconstituted tri-nucleosomes mimicking a centromeric nucleosome arrangement containing the CENP-A nucleosome, and determined their 3D structures by cryoelectron microscopy. The H3-CENP-A-H3 tri-nucleosomes adopt an untwisted architecture, with an outward-facing linker DNA path between nucleosomes. This is distinct from the H3-H3-H3 tri-nucleosome architecture, with an inward-facing DNA path. Intriguingly, the untwisted architecture may allow the CENP-A nucleosome to be exposed to the solvent in the condensed chromatin model. These results provide a structural basis for understanding the 3D configuration of CENP-A-containing chromatin, and may explain how centromeric proteins can specifically target the CENP-A nucleosomes buried in robust amounts of H3 nucleosomes in centromeres.


    Organizational Affiliation

    Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address: kurumizaka@iam.u-tokyo.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1A, E, K, O, S, W139Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4B, F, L, P, T, X106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
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PHAROS  P62805
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/EC, G, M, Q, U, Y133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
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PHAROS  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-JD, H, N, R, V, Z129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS  P06899
Protein Feature View
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganism
DNA (485-MER)I485synthetic construct

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA (485-MER)J485synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP18H05534
Japan Society for the Promotion of ScienceJapanJP17H01408
Japan Society for the Promotion of ScienceJapanJP17H05013
Japan Society for the Promotion of ScienceJapan17H06167
Japan Society for the Promotion of ScienceJapan15H05972
Japan Society for the Promotion of ScienceJapanJP19K06522

Revision History 

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references