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- PDB-9s5j: Portal and adaptor protein of bacteriophage LUZ19 computed in C12... -

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Basic information

Entry
Database: PDB / ID: 9s5j
TitlePortal and adaptor protein of bacteriophage LUZ19 computed in C12 symmetry
Components
  • adaptor protein
  • portal protein
KeywordsSTRUCTURAL PROTEIN / portal protein / adaptor protein / connector
Biological speciesPseudomonas phage LUZ19 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsStefanik Sobotkova, A. / Cienikova, Z. / Mironova, Y. / Fuzik, T. / Plevka, P. / Novacek, J. / Hlavenkova, Z.
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. / Novacek, J. / Hlavenkova, Z.
History
DepositionJul 29, 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
A: portal protein
X: adaptor protein


Theoretical massNumber of molelcules
Total (without water)77,3802
Polymers77,3802
Non-polymers00
Water00
1
A: portal protein
X: adaptor protein
x 12


Theoretical massNumber of molelcules
Total (without water)928,56524
Polymers928,56524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11

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Components

#1: Protein portal protein


Mass: 56169.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus)
#2: Protein adaptor protein


Mass: 21211.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus)
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: 0.924 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21683 / Symmetry type: POINT

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