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- PDB-9qg7: In situ structure of the Vaccinia virus (WR) portal complex in ma... -

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Basic information

Entry
Database: PDB / ID: 9qg7
TitleIn situ structure of the Vaccinia virus (WR) portal complex in mature virions
Components
  • Core protein A10
  • Core protein A4
  • Portal Protein E6
  • Portal Protein L3
  • Portal protein E8
KeywordsVIRAL PROTEIN / portal complex / morphogenesis / assembly / translation
Function / homology
Function and homology information


virion assembly / virion component / host cell cytoplasm / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell endoplasmic reticulum membrane / structural molecule activity
Similarity search - Function
Poxvirus L3/FP4 / Poxvirus E8 / Pox virus E6 protein / Poxvirus L3/FP4 protein / Poxvirus E8 protein / Pox virus E6 protein / Orthopoxvirus A5 / Orthopoxvirus A5L protein-like / Poxvirus P4A / Poxvirus P4A protein
Similarity search - Domain/homology
Protein OPG097 / Major core protein OPG136 precursor / Protein OPG068 / Protein OPG070 / 39kDa core protein OPG130
Similarity search - Component
Biological speciesVaccinia virus WR
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.21 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: To Be Published
Title: In situ structure of the poxvirus portal complex
Authors: Calcraft, T. / Hernandez-Gonzalez, M. / Nans, A. / Rosenthal, P.B. / Way, M.
History
DepositionMar 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein E8
B: Portal Protein E6
C: Portal Protein L3
D: Portal Protein L3
E: Core protein A10
F: Core protein A4
G: Core protein A10
H: Core protein A4
I: Core protein A10
J: Core protein A4
K: Portal protein E8
L: Portal Protein E6
M: Portal Protein L3
N: Portal Protein L3
O: Core protein A10
P: Core protein A4
Q: Core protein A10
R: Core protein A4
S: Core protein A10
T: Core protein A4
U: Portal protein E8
V: Portal Protein E6
W: Portal Protein L3
X: Portal Protein L3
Y: Core protein A10
Z: Core protein A4
a: Core protein A10
b: Core protein A4
c: Core protein A10
d: Core protein A4
e: Portal protein E8
f: Portal Protein E6
g: Portal Protein L3
h: Portal Protein L3
i: Core protein A10
j: Core protein A4
k: Core protein A10
l: Core protein A4
m: Core protein A10
n: Core protein A4
o: Portal protein E8
p: Portal Protein E6
q: Portal Protein L3
r: Portal Protein L3
s: Core protein A10
t: Core protein A4
u: Core protein A10
v: Core protein A4
w: Core protein A10
x: Core protein A4
y: Portal protein E8
z: Portal Protein E6
1: Portal Protein L3
2: Portal Protein L3
3: Core protein A10
4: Core protein A4
5: Core protein A10
6: Core protein A4
7: Core protein A10
8: Core protein A4


Theoretical massNumber of molelcules
Total (without water)2,310,86660
Polymers2,310,86660
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Portal protein E8 / Protein OPG070


Mass: 31791.479 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vaccinia virus WR / References: UniProt: P23372
#2: Protein
Portal Protein E6 / Protein OPG068


Mass: 66812.773 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vaccinia virus WR / References: UniProt: P21607
#3: Protein
Portal Protein L3 / Protein OPG097 / Protein F4


Mass: 33045.363 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Vaccinia virus WR / References: UniProt: P07614
#4: Protein
Core protein A10 / Major core protein OPG136 precursor / p4a / Virion core protein 4a precursor


Mass: 68417.578 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Vaccinia virus WR / References: UniProt: P16715
#5: Protein/peptide
Core protein A4 / p39 / 39kDa core protein OPG130


Mass: 5065.543 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Vaccinia virus WR / References: UniProt: P29191
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Portal complex with surrounding palisade trimersCOMPLEXall0NATURAL
2Portal complexCOMPLEX#1-#31NATURAL
3Palisade trimersCOMPLEX#4-#51NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Vaccinia virus WR10254A36-YdF
32Vaccinia virus WR10254
43Vaccinia virus WR10254
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 45mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.4 e/Å2 / Avg electron dose per subtomogram: 98.4 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameCategoryDetails (eV)
1PyTomvolume selection
2EMAN2volume selection
3UCSF ChimeraXvolume selectionArtiaX
4RELIONvolume selection
5FEI tomographyimage acquisition
7GctfCTF correction
8RELIONCTF correction
11ISOLDEmodel fitting
14RELIONfinal Euler assignment
16RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 8.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2075 / Algorithm: FOURIER SPACE / Symmetry type: POINT
EM volume selectionMethod: Template matching / Details: Template matching and interactive curation / Num. of tomograms: 100 / Num. of volumes extracted: 5369 / Reference model: EMD-18917
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDSource nameTypeAccession codeInitial refinement model-ID
11AlphaFoldin silico model
21AlphaFoldin silico model
31AlphaFoldin silico model
48R5I

8r5i

1PDBexperimental model8R5I2

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