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- PDB-9b41: Pseudomonas phage Pa193 Neck (portal and head-to-tail proteins) -

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Basic information

Entry
Database: PDB / ID: 9b41
TitlePseudomonas phage Pa193 Neck (portal and head-to-tail proteins)
Components
  • gp19 Portal
  • gp28 Head-to-tail protein
KeywordsVIRAL PROTEIN / phage / bacteriophage / gene product (gp19) / STRUCTURAL PROTEIN / gene product 28 (gp28) / head-to-tail protein / portal protein
Function / homologyInorganic pyrophosphatase domain / Inorganic Pyrophosphatase / Protein of unknown function DUF4054 / Protein of unknown function (DUF4054) / Protein of unknown function DUF1073 / Phage portal protein / Phage protein / Inorganic pyrophosphatase domain-containing protein
Function and homology information
Biological speciesPseudomonas virus Pa193
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsIglesias, S.M. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM140733 United States
CitationJournal: Commun Biol / Year: 2024
Title: Cryo-EM analysis of Pseudomonas phage Pa193 structural components.
Authors: Stephano M Iglesias / Chun-Feng David Hou / Johnny Reid / Evan Schauer / Renae Geier / Angela Soriaga / Lucy Sim / Lucy Gao / Julian Whitelegge / Pierre Kyme / Deborah Birx / Sebastien Lemire / Gino Cingolani /
Abstract: The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various ...The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.
History
DepositionMar 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: gp19 Portal
A: gp19 Portal
B: gp19 Portal
C: gp19 Portal
D: gp19 Portal
E: gp19 Portal
F: gp19 Portal
G: gp19 Portal
H: gp19 Portal
I: gp19 Portal
J: gp19 Portal
K: gp19 Portal
M: gp28 Head-to-tail protein
N: gp28 Head-to-tail protein
O: gp28 Head-to-tail protein
P: gp28 Head-to-tail protein
Q: gp28 Head-to-tail protein
R: gp28 Head-to-tail protein
S: gp28 Head-to-tail protein
T: gp28 Head-to-tail protein
U: gp28 Head-to-tail protein
V: gp28 Head-to-tail protein
W: gp28 Head-to-tail protein
X: gp28 Head-to-tail protein


Theoretical massNumber of molelcules
Total (without water)1,216,36524
Polymers1,216,36524
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
gp19 Portal


Mass: 84478.500 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KVD8
#2: Protein
gp28 Head-to-tail protein


Mass: 16885.285 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KV97
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 virus Pa193 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas virus Pa193
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 magnification: 64000 X / Calibrated magnification: 64000 X / Nominal defocus max: 1750 nm / Nominal defocus min: 750 nm / Calibrated defocus min: 750 nm / Calibrated defocus max: 1750 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 34.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 12520

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
4RELION4CTF correction
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 46075
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9179 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT

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