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- PDB-8wdc: Structural organization of the palisade layer in intracellular ma... -

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Basic information

Entry
Database: PDB / ID: 8wdc
TitleStructural organization of the palisade layer in intracellular mature vaccinia virions
ComponentsCore protein OPG136
KeywordsVIRAL PROTEIN / poxvirus / assembly / core / palisade layer / A10
Function / homologyPoxvirus P4A / Poxvirus P4A protein / virion component / structural molecule activity / Major core protein OPG136 precursor
Function and homology information
Biological speciesVaccinia virus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.7 Å
AuthorsLiu, Y. / Qu, X. / Duan, M. / Shi, X. / Liu, S. / Shi, Y. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Cryo-ET reveals A10 protein as a major component of the poxvirus palisade layer
Authors: Liu, Y. / Qu, X. / Duan, M. / Shi, X. / Liu, S. / Shi, Y. / Gao, G.F.
History
DepositionSep 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core protein OPG136
B: Core protein OPG136
C: Core protein OPG136


Theoretical massNumber of molelcules
Total (without water)213,2203
Polymers213,2203
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 Core protein OPG136 / 62 kDa peptide / Coordinate model: Cα atoms only


Mass: 71073.477 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Vaccinia virus (strain Western Reserve) / Cell line: grown in HeLa cells / References: UniProt: P16715

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Vaccinia virus Western Reserve / Type: VIRUS
Details: Vaccinia virus was grown in HeLa cells and purified.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Vaccinia virus Western Reserve
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 9 / Details: 1mM Tris pH 9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Vaccinia virus was grown in HeLa cells and purified. The resultant mature virions were used as a specimen.
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: 53000 X / Nominal defocus max: 3700 nm / Nominal defocus min: 1600 nm / Cs: 0 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.9 e/Å2 / Avg electron dose per subtomogram: 119 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Details: Dose rate 5.2 e-/pixel/s, EER (241 frames/sec)
EM imaging opticsEnergyfilter name: TFS Selectris X
Chromatic aberration corrector: Microscope was equipped with a Cc corrector
Details: about 20% of tilt series were collected using a slit width of 60 ev
Energyfilter slit width: 40 eV
Spherical aberration corrector: Microscope was equipped with a Cs corrector

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Processing

EM software
IDNameVersionCategoryDetails
1Dynamovolume selection
2SerialEM3.9image acquisition
4Warp1.1.0CTF correction
8UCSF Chimeramodel fittingRigid body fitting
12RELIONfinal Euler assignment
13Dynamofinal Euler assignment
15RELION3.133D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 602843 / Algorithm: FOURIER SPACE / Symmetry type: POINT
EM volume selectionDetails: Tomograms generated in Warp were denoised and corrected for missing wedge information using IsoNet. Subtomograms were selected by oversampling points at 4 nm distance using a surface model ...Details: Tomograms generated in Warp were denoised and corrected for missing wedge information using IsoNet. Subtomograms were selected by oversampling points at 4 nm distance using a surface model in Dynamo. In essence, for each viral core, a 3D surface was generated by fitting manually selected points on the core surface.
Num. of tomograms: 197 / Num. of volumes extracted: 1258156
Atomic model buildingSource name: AlphaFold / Type: in silico model

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