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- PDB-9cvt: Melbournevirus Mini variant Nucleosome -

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Basic information

Entry
Database: PDB / ID: 9cvt
TitleMelbournevirus Mini variant Nucleosome
Components
  • Histone doublet H4-H3
  • Histone doublet miniH2B-H2A
  • Widom 601 Strand 1
  • Widom 601 Strand 2
KeywordsVIRAL PROTEIN/DNA / Histone / Nucleosome / Virus / VIRAL PROTEIN / VIRAL 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 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 miniH2B-H2A / Histone doublet H4-H3
Similarity search - Component
Biological speciesMelbournevirus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.41 Å
AuthorsVillalta, A. / Luger, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Melbournevirus Mini variant Nucleosome
Authors: Villalta, A. / Luger, K.
History
DepositionJul 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone doublet miniH2B-H2A
B: Histone doublet miniH2B-H2A
C: Histone doublet H4-H3
D: Histone doublet H4-H3
I: Widom 601 Strand 1
J: Widom 601 Strand 2


Theoretical massNumber of molelcules
Total (without water)176,2146
Polymers176,2146
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Histone doublet miniH2B-H2A / Histone miniH2B-H2A fusion protein / MV-miniH2B-H2A


Mass: 19168.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melbournevirus / Gene: MEL_149 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A097I1R9
#2: Protein Histone doublet H4-H3 / Histone H4-H3 fusion protein / MV-H4-H3


Mass: 23564.680 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
#3: DNA chain Widom 601 Strand 1


Mass: 45153.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: DNA chain Widom 601 Strand 2


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

Component
IDNameTypeEntity IDParent-IDSource
1Melbourne nucleosome mini variantCOMPLEXall0MULTIPLE SOURCES
2Melbourne nucleosome mini variant histone doublet proteinsCOMPLEX#1-#21RECOMBINANT
3Widom 601 DNACOMPLEX#3-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Melbournevirus1560514
33synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 / Nominal defocus max: 20000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36051 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049417
ELECTRON MICROSCOPYf_angle_d0.70613464
ELECTRON MICROSCOPYf_dihedral_angle_d32.9622504
ELECTRON MICROSCOPYf_chiral_restr0.0381561
ELECTRON MICROSCOPYf_plane_restr0.0041049

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