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- PDB-9b42: Pseudomonas phage Pa193 neck and extended tail (collar, gateway, ... -

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Basic information

Entry
Database: PDB / ID: 9b42
TitlePseudomonas phage Pa193 neck and extended tail (collar, gateway, tail tube, and sheath proteins)
Components
  • gp29 Collar
  • gp30 Gateway
  • gp32 Sheath
  • gp33 Tail tube
KeywordsVIRAL PROTEIN / phage / bacteriophage / gene product (gp29) / STRUCTURAL PROTEIN / gene product 30 (gp30) / collar protein / gateway protein / sheath protein / tail tube protein / gene product 32 (gp32) / gene product 33 (gp33)
Function / homology
Function and homology information


: / : / E217 collar protein gp28 / E217 gateway protein gp29 / : / Tail fiber protein gp32 / Protein of unknown function DUF3383 / Protein of unknown function (DUF3383)
Similarity search - Domain/homology
Virion protein / Tail sheath protein / Phage protein / Tail fiber protein
Similarity search - Component
Biological speciesPseudomonas virus Pa193
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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
S: gp32 Sheath
A: gp29 Collar
B: gp29 Collar
C: gp29 Collar
D: gp29 Collar
E: gp29 Collar
F: gp29 Collar
M: gp33 Tail tube
N: gp33 Tail tube
O: gp33 Tail tube
P: gp33 Tail tube
Q: gp33 Tail tube
R: gp33 Tail tube
J: gp30 Gateway
G: gp30 Gateway
H: gp30 Gateway
I: gp30 Gateway
K: gp30 Gateway
L: gp30 Gateway


Theoretical massNumber of molelcules
Total (without water)368,45119
Polymers368,45119
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 gp32 Sheath


Mass: 53840.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KVA0
#2: Protein
gp29 Collar


Mass: 15325.353 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KV91
#3: Protein
gp33 Tail tube


Mass: 15905.042 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KYR7
#4: Protein
gp30 Gateway


Mass: 21204.689 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KVE6
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
Natural hostOrganism: Pseudomonas aeruginosa
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: OTHER
Electron lensMode: OTHER / 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: C6 (6 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9179 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 60.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005826505
ELECTRON MICROSCOPYf_angle_d0.863736008
ELECTRON MICROSCOPYf_chiral_restr0.05544024
ELECTRON MICROSCOPYf_plane_restr0.00624726
ELECTRON MICROSCOPYf_dihedral_angle_d5.62963541

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