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- PDB-7yjl: Melbournevirus major capsid protein built from 4.4A reconstruction -

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Basic information

Entry
Database: PDB / ID: 7yjl
TitleMelbournevirus major capsid protein built from 4.4A reconstruction
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / MCP / Melbournevirus / giant virus / major capsid protein
Function / homologyMajor capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesMelbournevirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.42 Å
AuthorsBurton-Smith, R.N. / Okamoto, K. / Murata, K.
Funding support Japan, Sweden, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H04845 Japan
Swedish Research Council2018-03387 Sweden
The Swedish Foundation for Strategic ResearchJA2014-5721 Sweden
Swedish Research Council2018-00421 Sweden
CitationJournal: To Be Published
Title: The 4.4A structure of the giant Melbournevirus virion belonging to the Marseilleviridae family
Authors: Burton-Smith, R.N. / Reddy, H.K.N. / Svenda, M. / Abergel, C. / Okamoto, K. / Murata, K.
History
DepositionJul 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)50,8971
Polymers50,8971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Major capsid protein


Mass: 50896.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Melbournevirus / References: UniProt: A0A097I267
Has protein modificationN

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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: Melbournevirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Melbournevirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
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: 3000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Image recordingElectron dose: 26.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187440 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0077180
ELECTRON MICROSCOPYf_angle_d0.86312903
ELECTRON MICROSCOPYf_dihedral_angle_d16.0952931
ELECTRON MICROSCOPYf_chiral_restr0.051568
ELECTRON MICROSCOPYf_plane_restr0.0051089

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