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- PDB-7xyc: CryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 ... -

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Basic information

Entry
Database: PDB / ID: 7xyc
TitleCryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 in vitro
Componentsphage tail fiber
KeywordsVIRAL PROTEIN / Phage type II tail fiber
Biological speciesKlebsiella phage Kp7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 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
A: phage tail fiber
B: phage tail fiber
C: phage tail fiber


Theoretical massNumber of molelcules
Total (without water)183,6313
Polymers183,6313
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein phage tail fiber


Mass: 61210.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage Kp7 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta

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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 II tail fiber / Type: COMPLEX / Details: Trimer of tail fiber proteins / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella phage Kp7 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta
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 R1.2/1.3
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 1800 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 ONLY
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113834 / Symmetry type: POINT
Atomic model buildingB value: 146 / Protocol: AB INITIO MODEL / Space: REAL

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