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- PDB-8feh: CryoEM structure of bacteriophage Q-beta coat protein dimer with ... -

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Basic information

Entry
Database: PDB / ID: 8feh
TitleCryoEM structure of bacteriophage Q-beta coat protein dimer with AYGG linker
ComponentsMinor capsid protein A1 fusion
KeywordsVIRUS LIKE PARTICLE / coat protein / q-beta / fusion
Function / homologyRead-through domain / Read-through domain / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / viral capsid / structural molecule activity / Minor capsid protein A1
Function and homology information
Biological speciesQubevirus durum
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsNewton, T.P. / Zhao, L. / Finn, M.G. / Kopylov, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: To Be Published
Title: CryoEM structure of bacteriophage Q-beta coat protein dimer with AYGG linker
Authors: Newton, T.P. / Zhao, L. / Kopylov, M. / Finn, M.G.
History
DepositionDec 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Minor capsid protein A1 fusion


Theoretical massNumber of molelcules
Total (without water)28,6041
Polymers28,6041
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Minor capsid protein A1 fusion / A1 read-through protein


Mass: 28604.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Qubevirus durum / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE1

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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: Qubevirus durum / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Qubevirus durum
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 0.001 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 64.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 3838 / Height: 3710

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1380 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT

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