7KBE

Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)

  • Classification: DNA BINDING PROTEIN/DNA
  • Organism(s): Xenopus laevis
  • Mutation(s): No 

  • Deposited: 2020-10-02 Released: 2021-09-15 
  • Deposition Author(s): Arimura, Y., Funabiki, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Structural features of nucleosomes in interphase and metaphase chromosomes.

Arimura, Y.Shih, R.M.Froom, R.Funabiki, H.

(2021) Mol Cell 81: 4377

  • DOI: https://doi.org/10.1016/j.molcel.2021.08.010
  • Primary Citation of Related Structures:  
    7KBD, 7KBE, 7KBF

  • PubMed Abstract: 

    Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.


  • Organizational Affiliation

    Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: yarimura@rockefeller.edu.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
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UniProt GroupP84233
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
139Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q6DKE3 (Xenopus laevis)
Explore Q6DKE3 
Go to UniProtKB:  Q6DKE3
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UniProt GroupQ6DKE3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
126Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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UniProt GroupP02281
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (157-MER)156Xenopus laevis
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (157-MER)156Xenopus laevis
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM132111
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references