8UA7 | pdb_00008ua7

Medusavirus Nucleosome Core Particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Characterization of Medusavirus encoded histones reveals nucleosome-like structures and a unique linker histone.

Toner, C.M.Hoitsma, N.M.Weerawarana, S.Luger, K.

(2024) Nat Commun 15: 9138-9138

  • DOI: https://doi.org/10.1038/s41467-024-53364-5
  • Primary Citation of Related Structures:  
    8UA7

  • PubMed Abstract: 

    The organization of DNA into nucleosomes is a ubiquitous and ancestral feature that was once thought to be exclusive to the eukaryotic domain of life. Intriguingly, several representatives of the Nucleocytoplasmic Large DNA Viruses (NCLDV) encode histone-like proteins that in Melbournevirus were shown to form nucleosome-like particles. Medusavirus medusae (MM), a distantly related giant virus, encodes all four core histone proteins and, unique amongst most giant viruses, a putative acidic protein with two domains resembling eukaryotic linker histone H1. Here, we report the structure of nucleosomes assembled with MM histones and highlight similarities and differences with eukaryotic and Melbournevirus nucleosomes. Our structure provides insight into how variations in histone tail and loop lengths are accommodated within the context of the nucleosome. We show that MM-histones assemble into tri-nucleosome arrays, and that the putative linker histone H1 does not function in chromatin compaction. These findings expand our limited understanding of chromatin organization by virus-encoded histones.


  • Organizational Affiliation
    • Department of Biochemistry, University of Colorado at Boulder, 80309, Boulder, CO, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
196MedusavirusMutation(s): 0 
UniProt
Find proteins for A0A3T1CX62 (Acanthamoeba castellanii medusavirus J1)
Explore A0A3T1CX62 
Go to UniProtKB:  A0A3T1CX62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3T1CX62
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
125MedusavirusMutation(s): 0 
UniProt
Find proteins for A0A3T1CX47 (Acanthamoeba castellanii medusavirus J1)
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Go to UniProtKB:  A0A3T1CX47
Entity Groups  
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UniProt GroupA0A3T1CX47
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
266MedusavirusMutation(s): 0 
UniProt
Find proteins for A0A3T1CXA3 (Acanthamoeba castellanii medusavirus J1)
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UniProt GroupA0A3T1CXA3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
219MedusavirusMutation(s): 0 
UniProt
Find proteins for A0A3T1CWJ9 (Acanthamoeba castellanii medusavirus J1)
Explore A0A3T1CWJ9 
Go to UniProtKB:  A0A3T1CWJ9
Entity Groups  
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UniProt GroupA0A3T1CWJ9
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Entity ID: 5
MoleculeChains LengthOrganismImage
WIDOM 601 DNA strand 1205synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
WIDOM 601 DNA strand 2205synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-04
    Changes: Data collection