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- PDB-7lv8: Structure of the Marseillevirus nucleosome -

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Basic information

Entry
Database: PDB / ID: 7lv8
TitleStructure of the Marseillevirus nucleosome
Components
  • (DNA (123-MER)) x 2
  • (Histone doublet Beta-Alpha ...) x 2
  • (Histone doublet Delta-Gamma ...) x 2
KeywordsSTRUCTURAL PROTEIN/DNA / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / protein heterodimerization activity / DNA binding
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone 2A / Histone H2A / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B/H2A fusion protein / Histone H3 / Histone H2B/H2A fusion protein
Similarity search - Component
Biological speciesMarseillevirus marseillevirus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsValencia-Sanchez, M.I. / Abini-Agbomson, S. / Armache, K.-J.
Funding support United States, 2items
OrganizationGrant numberCountry
David and Lucile Packard Foundationna United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM115882-03 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: The structure of a virus-encoded nucleosome.
Authors: Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Miao Wang / Rachel Lee / Nikita Vasilyev / Jenny Zhang / Pablo De Ioannes / Bernard La Scola / Paul Talbert / Steve Henikoff / Evgeny ...Authors: Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Miao Wang / Rachel Lee / Nikita Vasilyev / Jenny Zhang / Pablo De Ioannes / Bernard La Scola / Paul Talbert / Steve Henikoff / Evgeny Nudler / Albert Erives / Karim-Jean Armache /
Abstract: Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to ...Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to the eukaryotic histone pairs H2B-H2A and H4-H3. These viral histones form 'forced' heterodimers, and a heterotetramer of four such heterodimers assembles DNA to form structures virtually identical to canonical eukaryotic nucleosomes.
History
DepositionFeb 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 26, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-23529
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Histone doublet Delta-Gamma (Delta)
A: Histone doublet Delta-Gamma (Gamma)
D: Histone doublet Beta-Alpha (Beta)
C: Histone doublet Beta-Alpha (Alpha)
F: Histone doublet Delta-Gamma (Delta)
E: Histone doublet Delta-Gamma (Gamma)
H: Histone doublet Beta-Alpha (Beta)
G: Histone doublet Beta-Alpha (Alpha)
I: DNA (123-MER)
J: DNA (123-MER)


Theoretical massNumber of molelcules
Total (without water)176,95110
Polymers176,95110
Non-polymers00
Water00
1


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

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Components

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Histone doublet Delta-Gamma ... , 2 types, 4 molecules BFAE

#1: Protein Histone doublet Delta-Gamma (Delta) / Histone H3


Mass: 10462.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marseillevirus marseillevirus / Gene: MAR_ORF413 / Production host: Escherichia coli (E. coli) / References: UniProt: D2XB48
#2: Protein Histone doublet Delta-Gamma (Gamma) / Histone H3


Mass: 11767.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marseillevirus marseillevirus / Gene: MAR_ORF413 / Production host: Escherichia coli (E. coli) / References: UniProt: D2XB48

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Histone doublet Beta-Alpha ... , 2 types, 4 molecules DHCG

#3: Protein Histone doublet Beta-Alpha (Beta) / Histone H2B/H2A fusion protein


Mass: 11228.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marseillevirus marseillevirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R3ZQX0
#4: Protein Histone doublet Beta-Alpha (Alpha) / Histone H2B/H2A fusion protein


Mass: 17675.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marseillevirus marseillevirus / Gene: MAR_ORF414 / Production host: Escherichia coli (E. coli) / References: UniProt: D2XB49

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (123-MER)


Mass: 37530.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (123-MER)


Mass: 37152.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has protein modificationY

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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

ComponentName: Structure of the Marseillevirus nucleosome / Type: COMPLEX / Details: virus-encoded histone doublets Marseillevirus / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21synthetic construct (others)32630
11Marseillevirus marseillevirus694581
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepesHepes1
21 mMEDTAEDTA1
32 mMDTTDTT1
SpecimenConc.: 3.3 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: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4503
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFINDcryoSPARCCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11cryoSPARC2.15initial Euler assignment
12cryoSPARC2.15final Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3017414
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146506 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
11KX5

1kx5

1KX51
23LZ0

3lz0

I3LZ02
33LZ0

3lz0

J3LZ02
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311353
ELECTRON MICROSCOPYf_angle_d0.62216345
ELECTRON MICROSCOPYf_dihedral_angle_d30.6053226
ELECTRON MICROSCOPYf_chiral_restr0.0371893
ELECTRON MICROSCOPYf_plane_restr0.0041220

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