7KBF

H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)

  • Classification: DNA BINDING PROTEIN
  • 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: 4.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 

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

  • 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 ...

    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: funabih@rockefeller.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G139Xenopus laevisMutation(s): 0 
Gene Names: h2ac1.Sh2ac1hist1h2aaMGC81997XELAEV_18014220mgXELAEV_18014222mg
UniProt
Find proteins for Q6DKE3 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H126Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Protein B4K273Xenopus laevisMutation(s): 0 
Gene Names: b4
UniProt
Find proteins for P15308 (Xenopus laevis)
Explore P15308 
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (184-MER)I172Xenopus laevis
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (184-MER)J172Xenopus laevis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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)JapanJSPS Overseas Research Fellowships

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release