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- PDB-9sys: Special vertex of bacteriophage LUZ19 computed in C1 symmetry -

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Basic information

Entry
Database: PDB / ID: 9sys
TitleSpecial vertex of bacteriophage LUZ19 computed in C1 symmetry
Components
  • Head-tail connector protein
  • Major capsid protein
  • Tail tubular protein A
KeywordsSTRUCTURAL PROTEIN / special vertex / portal / adaptor / capsid / connector
Function / homologyTail tubular protein Gp11 / Tail tubular protein / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / symbiont genome ejection through host cell envelope, short tail mechanism / virion component / Head-tail connector protein / Major capsid protein / Tail tubular protein A
Function and homology information
Biological speciesPseudomonas phage LUZ19 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.01 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
DepositionOct 14, 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

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Tail tubular protein A
Q: Tail tubular protein A
R: Tail tubular protein A
S: Tail tubular protein A
T: Tail tubular protein A
U: Tail tubular protein A
V: Tail tubular protein A
W: Tail tubular protein A
X: Tail tubular protein A
Y: Head-tail connector protein
Z: Head-tail connector protein
a: Head-tail connector protein
b: Head-tail connector protein
c: Head-tail connector protein
d: Head-tail connector protein
e: Head-tail connector protein
f: Head-tail connector protein
g: Head-tail connector protein
h: Head-tail connector protein
i: Head-tail connector protein
j: Head-tail connector protein
k: Tail tubular protein A
l: Tail tubular protein A
m: Tail tubular protein A


Theoretical massNumber of molelcules
Total (without water)1,494,97839
Polymers1,494,97839
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Major capsid protein


Mass: 37760.891 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7B7
#2: Protein
Tail tubular protein A


Mass: 21211.096 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7B9
#3: Protein
Head-tail connector protein


Mass: 56169.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage LUZ19 (virus) / References: UniProt: A9J7B4
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: 1.494 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: 4.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21683 / Symmetry type: POINT

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