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- PDB-7y1c: CryoEM structure of Klebsiella phage Kp9 tail complex applied wit... -

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Basic information

Entry
Database: PDB / ID: 7y1c
TitleCryoEM structure of Klebsiella phage Kp9 tail complex applied with C6 symmetry
Components
  • phage connector protein
  • phage tail tubular protein A
  • phage tail tubular protein B
  • phage type I tail fiber
KeywordsVIRUS / Complex / Podophage / short non-contractile tail
Biological speciesKlebsiella phage Kp9 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 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 8, 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

Downloads & links

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Assembly

Deposited unit
A: phage connector protein
L: phage connector protein
W: phage tail tubular protein A
X: phage tail tubular protein A
Y: phage tail tubular protein B
e: phage type I tail fiber
f: phage type I tail fiber
g: phage type I tail fiber


Theoretical massNumber of molelcules
Total (without water)501,5158
Polymers501,5158
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 connector protein


Mass: 58661.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp9 (virus)
#2: Protein phage tail tubular protein A


Mass: 21374.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp9 (virus)
#3: Protein phage tail tubular protein B


Mass: 89081.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp9 (virus)
#4: Protein phage type I tail fiber


Mass: 84120.445 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp9 (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 Kp9 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella phage Kp9 (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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Image scansWidth: 5760 / Height: 4092

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Processing

EM softwareName: RELION / Version: 3.0.8 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41926 / Symmetry type: POINT
Atomic model buildingB value: 63 / Protocol: AB INITIO MODEL / Space: REAL

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