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- PDB-9ay3: Tail sheath of P1 bacteriophage -

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Basic information

Entry
Database: PDB / ID: 9ay3
TitleTail sheath of P1 bacteriophage
ComponentsGp22
KeywordsVIRAL PROTEIN / P1 bacteriophage / tail sheath / tail tube / contractile protein / structural protein
Function / homologyGp22
Function and homology information
Biological speciesEscherichia phage P1 (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsNakamura, T. / Sen, A. / Terashi, G. / Kihara, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM133840 United States
CitationJournal: To Be Published
Title: Tail sheath of P1 bacteriophage
Authors: Nakamura, T. / Sen, A. / Terashi, G. / Kihara, D.
History
DepositionMar 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp22
B: Gp22
C: Gp22
D: Gp22
E: Gp22
F: Gp22
G: Gp22
H: Gp22
I: Gp22
J: Gp22
K: Gp22
L: Gp22
M: Gp22
N: Gp22
O: Gp22
P: Gp22
Q: Gp22
R: Gp22


Theoretical massNumber of molelcules
Total (without water)1,025,80618
Polymers1,025,80618
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
Gp22


Mass: 56989.246 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage P1 (virus) / Gene: 22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q71TB2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Escherichia phage P1 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage P1 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 19.32 ° / Axial rise/subunit: 39.15 Å / Axial symmetry: C6
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119472 / Symmetry type: HELICAL

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