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- PDB-7y3t: CryoEM structure of Klebsiella phage Kp7 icosahedral head -

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Basic information

Entry
Database: PDB / ID: 7y3t
TitleCryoEM structure of Klebsiella phage Kp7 icosahedral head
Componentsphage major capsid protein
KeywordsVIRUS / Podophage / icosahedral head
Biological speciesKlebsiella phage Kp7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHuang, L. / Xiang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure and assembly of the Klebsiella pneumoniae phage tail fibers
Authors: Huang, L. / Xiang, Y.
History
DepositionJun 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: phage major capsid protein
A: phage major capsid protein
B: phage major capsid protein
C: phage major capsid protein
D: phage major capsid protein
E: phage major capsid protein
F: phage major capsid protein


Theoretical massNumber of molelcules
Total (without water)278,2067
Polymers278,2067
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
phage major capsid protein


Mass: 39743.750 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp7 (virus)

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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: Klebsiella phage Kp7 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella phage Kp7 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Klebsiella pneumoniae ATCC 43816
Virus shellDiameter: 600 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 3710 / Height: 3710

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Processing

EM softwareName: RELION / Version: 3.0.8 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31647 / Symmetry type: POINT

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