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- PDB-9s0y: bacteriophage LUZ19 tail complex computed in C6 symmetry -

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Basic information

Entry
Database: PDB / ID: 9s0y
Titlebacteriophage LUZ19 tail complex computed in C6 symmetry
Components
  • Phage particle protein
  • Tail tubular protein B
  • tail channel protein
KeywordsSTRUCTURAL PROTEIN / tail protein / tail fibres / genome delivery
Function / homology: / Bacteriophage nozzle protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / virus tail / Uncharacterized protein gp29 / Tail tubular protein B / Phage particle protein
Function and homology information
Biological speciesPseudomonas phage LUZ19 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsStefanik Sobotkova, A. / Cienikova, Z. / Mironova, Y. / Fuzik, T. / Plevka, P. / Hlavenkova, Z. / Novacek, J.
Funding support Czech Republic, European Union, 2items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Structure of bacteriophage LUZ19 native particle
Authors: Stefanik Sobotkova, A. / Cienikova, Z. / Mironova, Y. / Fuzik, T. / Plevka, P. / Hlavenkova, Z. / Novacek, J.
History
DepositionJul 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 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

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Assembly

Deposited unit
AA: Tail tubular protein B
AB: Phage particle protein
AC: Phage particle protein
AD: Phage particle protein
AE: tail channel protein


Theoretical massNumber of molelcules
Total (without water)146,6135
Polymers146,6135
Non-polymers00
Water00
1
AA: Tail tubular protein B
AB: Phage particle protein
AC: Phage particle protein
AD: Phage particle protein
AE: tail channel protein
x 6


Theoretical massNumber of molelcules
Total (without water)879,67730
Polymers879,67730
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein Tail tubular protein B


Mass: 91887.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7C0
#2: Protein Phage particle protein


Mass: 15003.919 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7C7
#3: Protein tail channel protein


Mass: 9713.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7B2
Has protein modificationN

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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: Pseudomonas phage LUZ19 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.696 MDa / Experimental value: YES
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding 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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 94 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21683 / Symmetry type: POINT

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