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- PDB-8arh: In situ subtomogram average of Vaccinia virus (WR) D13 lattice, o... -

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Basic information

Entry
Database: PDB / ID: 8arh
TitleIn situ subtomogram average of Vaccinia virus (WR) D13 lattice, on immature virions
ComponentsScaffold protein D13
KeywordsVIRUS / Palisade / Lattice / A4
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus WR
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 19.2 Å
AuthorsCalcraft, T. / Hernandez-Gonzalez, M. / Nans, A. / Rosenthal, P.B. / Way, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: PLoS Biol / Year: 2023
Title: A succession of two viral lattices drives vaccinia virus assembly.
Authors: Miguel Hernandez-Gonzalez / Thomas Calcraft / Andrea Nans / Peter B Rosenthal / Michael Way /
Abstract: During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped ...During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virions (IMV) that lack D13. Here, we performed cryo-electron tomography (cryo-ET) of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation, a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. As maturation occurs, which involves a 50% reduction in particle volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _citation_author.identifier_ORCID
Revision 1.2Jul 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Scaffold protein D13
B: Scaffold protein D13
C: Scaffold protein D13
D: Scaffold protein D13
E: Scaffold protein D13
F: Scaffold protein D13


Theoretical massNumber of molelcules
Total (without water)371,6916
Polymers371,6916
Non-polymers00
Water00
1
A: Scaffold protein D13
B: Scaffold protein D13
C: Scaffold protein D13
D: Scaffold protein D13
E: Scaffold protein D13
F: Scaffold protein D13
x 6


Theoretical massNumber of molelcules
Total (without water)2,230,14736
Polymers2,230,14736
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
MethodUCSF CHIMERA

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Components

#1: Protein
Scaffold protein D13 / 62 kDa protein / Rifampicin resistance protein


Mass: 61948.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve / Gene: VACWR118, D13L / Cell line (production host): HeLa / Production host: Homo sapiens (human) / References: UniProt: P68440

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Vaccinia virus WR / Type: VIRUS / Details: A36-YdF deltaNPF1-3 deltaF11 / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Vaccinia virus WR
Source (recombinant)Organism: Homo sapiens (human) / Cell: HeLa
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 11600 X / Nominal defocus max: 8000 nm / Nominal defocus min: 8000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.7 e/Å2 / Avg electron dose per subtomogram: 66.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 4

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Processing

EM software
IDNameVersionCategory
2FEI tomographyimage acquisition
4CTFFINDCTF correction
5NOVACTFCTF correction
8UCSF ChimeraXmodel fitting
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 19.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34092 / Algorithm: FOURIER SPACE / Symmetry type: POINT
EM volume selectionNum. of tomograms: 13 / Num. of volumes extracted: 341376
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7VFE

7vfe


Accession code: 7VFE / Source name: PDB / Type: experimental model

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