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- EMDB-37456: Structural organization of the palisade layer in isolated vaccini... -

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Basic information

Entry
Database: EMDB / ID: EMD-37456
TitleStructural organization of the palisade layer in isolated vaccinia virus cores
Map data
Sample
  • Virus: Vaccinia virus Western Reserve
    • Protein or peptide: Core protein OPG136
Keywordspoxvirus / assembly / core / palisade layer / A10 / VIRAL PROTEIN
Function / homologyPoxvirus P4A / Poxvirus P4A protein / virion component / structural molecule activity / Major core protein OPG136 precursor
Function and homology information
Biological speciesVaccinia virus (strain Western Reserve) / Vaccinia virus Western Reserve
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 Å
AuthorsLiu Y / Qu X / Duan M / Shi X / Liu S / Shi Y / Gao GF
Funding support China, 1 items
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 GF
History
DepositionSep 14, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37456.png

Downloads & links

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Map

FileDownload / File: emd_37456.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 120 pix.
= 480. Å		4 Å/pix.
x 120 pix.
= 480. Å		4 Å/pix.
x 120 pix.
= 480. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0016
Minimum - Maximum-0.025322722 - 0.01429427
Average (Standard dev.)0.000042559517 (±0.0008079759)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37456_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_37456_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_37456_half_map_2.map
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Sample components

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Entire : Vaccinia virus Western Reserve

EntireName: Vaccinia virus Western Reserve
Components
  • Virus: Vaccinia virus Western Reserve
    • Protein or peptide: Core protein OPG136

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Supramolecule #1: Vaccinia virus Western Reserve

SupramoleculeName: Vaccinia virus Western Reserve / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Vaccinia virus was grown in HeLa cells and purified. The resultant mature virions were treated with DTT and NP40 and then purified to yield viral cores.
NCBI-ID: 696871 / Sci species name: Vaccinia virus Western Reserve / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Core protein OPG136

MacromoleculeName: Core protein OPG136 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus (strain Western Reserve)
Molecular weightTheoretical: 71.073477 KDa
SequenceString: MMPIKSIVTL DQLEDSEYLF RIVSTVLPHL CLDYKVCDQL KTTFVHPFDI LLNNSLGSVT KQDELQAAIS KLGINYLIDT TSRELKLFN VTLNAGNIDI INTPINISSE TNPIINTHSF YDLPPFTQHL LNIRLTDTEY RARFIGGYIK PDGSDSMDVL A EKKYPDLN ...String:
MMPIKSIVTL DQLEDSEYLF RIVSTVLPHL CLDYKVCDQL KTTFVHPFDI LLNNSLGSVT KQDELQAAIS KLGINYLIDT TSRELKLFN VTLNAGNIDI INTPINISSE TNPIINTHSF YDLPPFTQHL LNIRLTDTEY RARFIGGYIK PDGSDSMDVL A EKKYPDLN FDNTYLFNIL YKDVINAPIK EFKAKIVNGV LSRQDFDNLI GVRQYITIQD RPRFDDAYNI ADAARHYGVN LN TLPLPNV DLTTMPTYKH LIMFEQYFIY TYDRVDIYYN GNKMLFDDEI INFTISMRYQ SLIPRLVDFF PDIPVNNNIV LHT RDPQNA AVNVTVALPN VQFVDINRNN KFFINFFNLL AKEQRSTAIK VTKSMFWDGM DYEEYKSKNL QDMMFINSTC YVFG LYNHN NTTYCSILSD IISAEKTPIR VCLLPRVVGG KTVTNLISET LKSISSMTIR EFPRKDKSIM HIGLSETGFM RFFQL LRLM ADKPHETAIK EVVMAYVGIK LGDKGSPYYI RKESYQDFIY LLFASMGFKV TTRRSIMGSN NISIISIRPR VTKQYI VAT LMKTSCSKNE AEKLITSAFD LLNFMVSVSD FRDYQSYRQY RNYCPRYFYA G

UniProtKB: Major core protein OPG136 precursor

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 9 / Details: 1mM Tris pH 9
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsVaccinia virus was grown in HeLa cells and purified. The resultant mature virions were treated with DTT and NP40 and then purified to yield viral cores. Isolated cores were used as a specimen.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope was equipped with a Cs corrector
Chromatic aberration corrector: Microscope was equipped with a Cc corrector
Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 40 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.9 e/Å2 / Details: Dose rate 5.2 e-/pixel/s, EER (241 frames/sec)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.13) / Number subtomograms used: 207056
ExtractionNumber tomograms: 74 / Number images used: 572775 / Software - Name: Dynamo
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 ...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.
Final angle assignmentType: OTHER / Software: (Name: RELION, Dynamo)
Details: Initially based on particle position on the modelled 3D surface during particle picking in Dynamo, where the in plane rotation angle is randomized. Refinement of particle translation and ...Details: Initially based on particle position on the modelled 3D surface during particle picking in Dynamo, where the in plane rotation angle is randomized. Refinement of particle translation and orientation was performed in RELION 3.1.3.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8wd7:
Structural organization of the palisade layer in isolated vaccinia virus cores

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