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- PDB-28sd: portal - core interface of bacteriophage LUZ19 computed in C4 symmetry -

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Basic information

Entry
Database: PDB / ID: 28sd
Titleportal - core interface of bacteriophage LUZ19 computed in C4 symmetry
Components
  • (Internal virion protein) x 2
  • (UNK) x 2
  • Head-tail connector protein
KeywordsSTRUCTURAL PROTEIN / core / portal / ejectosome / connector
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope / symbiont genome ejection through host cell envelope, short tail mechanism / virion component / lysozyme activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Internal virion protein Gp14 / T7 virus internal virion protein gp14 family / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Head-tail connector protein / Internal virion protein / Internal virion protein
Similarity search - Component
Biological speciesPseudomonas phage LUZ19 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 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
DepositionFeb 17, 2026Deposition 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

Downloads & links

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Assembly

Deposited unit
K: Head-tail connector protein
P: Head-tail connector protein
T: Head-tail connector protein
C: Internal virion protein
G: Internal virion protein
a: Internal virion protein
b: Internal virion protein
e: UNK
f: UNK


Theoretical massNumber of molelcules
Total (without water)406,4759
Polymers406,4759
Non-polymers00
Water00
1
K: Head-tail connector protein
P: Head-tail connector protein
T: Head-tail connector protein
C: Internal virion protein
G: Internal virion protein
a: Internal virion protein
b: Internal virion protein
e: UNK
f: UNK

K: Head-tail connector protein
P: Head-tail connector protein
T: Head-tail connector protein
C: Internal virion protein
G: Internal virion protein
a: Internal virion protein
b: Internal virion protein
e: UNK
f: UNK

K: Head-tail connector protein
P: Head-tail connector protein
T: Head-tail connector protein
C: Internal virion protein
G: Internal virion protein
a: Internal virion protein
b: Internal virion protein
e: UNK
f: UNK

K: Head-tail connector protein
P: Head-tail connector protein
T: Head-tail connector protein
C: Internal virion protein
G: Internal virion protein
a: Internal virion protein
b: Internal virion protein
e: UNK
f: UNK


Theoretical massNumber of molelcules
Total (without water)1,625,90136
Polymers1,625,90136
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3

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Components

#1: Protein Head-tail connector protein


Mass: 56169.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7B4
#2: Protein Internal virion protein


Mass: 18852.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7C2
#3: Protein Internal virion protein


Mass: 98368.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7C3
#4: Protein/peptide UNK


Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus)
#5: Protein/peptide UNK


Mass: 1890.321 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: 0.402 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
IDNameVersionCategory
1crYOLOparticle selection
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18360 / Symmetry type: POINT

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