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- PDB-7n8n: Melbournevirus nucleosome like particle -

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Basic information

Entry
Database: PDB / ID: 7n8n
TitleMelbournevirus nucleosome like particle
Components
  • (DNA (147-MER)) x 2
  • Histone H2B-H2A doublet
  • Histone H4-H3 doublet
KeywordsDNA BINDING PROTEIN/DNA / nucleosome / Virus / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


chromosome condensation / virion component / structural constituent of chromatin / host cell cytoplasm / protein heterodimerization activity / host cell nucleus / DNA binding
Similarity search - Function
Histone H2A / Histone 2A / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone doublet H2B-H2A / Histone doublet H4-H3
Similarity search - Component
Biological speciesMelbournevirus
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsLiu, Y. / Toner, C.M. / Zhou, K. / Bowerman, S. / Luger, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2021
Title: Virus-encoded histone doublets are essential and form nucleosome-like structures.
Authors: Yang Liu / Hugo Bisio / Chelsea Marie Toner / Sandra Jeudy / Nadege Philippe / Keda Zhou / Samuel Bowerman / Alison White / Garrett Edwards / Chantal Abergel / Karolin Luger /
Abstract: The organization of genomic DNA into defined nucleosomes has long been viewed as a hallmark of eukaryotes. This paradigm has been challenged by the identification of "minimalist" histones in archaea ...The organization of genomic DNA into defined nucleosomes has long been viewed as a hallmark of eukaryotes. This paradigm has been challenged by the identification of "minimalist" histones in archaea and more recently by the discovery of genes that encode fused remote homologs of the four eukaryotic histones in Marseilleviridae, a subfamily of giant viruses that infect amoebae. We demonstrate that viral doublet histones are essential for viral infectivity, localize to cytoplasmic viral factories after virus infection, and ultimately are found in the mature virions. Cryogenic electron microscopy (cryo-EM) structures of viral nucleosome-like particles show strong similarities to eukaryotic nucleosomes despite the limited sequence identify. The unique connectors that link the histone chains contribute to the observed instability of viral nucleosomes, and some histone tails assume structural roles. Our results further expand the range of "organisms" that require nucleosomes and suggest a specialized function of histones in the biology of these unusual viruses.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Histone H4-H3 doublet
B: Histone H2B-H2A doublet
C: Histone H4-H3 doublet
D: Histone H2B-H2A doublet
I: DNA (147-MER)
J: DNA (147-MER)


Theoretical massNumber of molelcules
Total (without water)208,3396
Polymers208,3396
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Histone H4-H3 doublet


Mass: 26737.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melbournevirus / Gene: MEL_368 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A097I2D0
#2: Protein Histone H2B-H2A doublet


Mass: 32058.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melbournevirus / Gene: MEL_369 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A097I2B5
#3: DNA chain DNA (147-MER)


Mass: 45153.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: DNA chain DNA (147-MER)


Mass: 45594.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Melbournevirus nucleosome like particleCOMPLEXall0MULTIPLE SOURCES
2Histone H4-H3 doublet, Histone H2B-H2A doubletCOMPLEX#1-#21RECOMBINANT
3DNA 147-merCOMPLEX#3-#41RECOMBINANT
Molecular weightValue: 0.218 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Melbournevirus1560514
23Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34418 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00611812
ELECTRON MICROSCOPYf_angle_d0.8116997
ELECTRON MICROSCOPYf_dihedral_angle_d32.5883388
ELECTRON MICROSCOPYf_chiral_restr0.0421964
ELECTRON MICROSCOPYf_plane_restr0.0061276

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