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- PDB-9b40: Pseudomonas phage Pa193 5-fold vertex (capsid, decorating, and sc... -

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Basic information

Entry
Database: PDB / ID: 9b40
TitlePseudomonas phage Pa193 5-fold vertex (capsid, decorating, and scaffolding proteins)
Components
  • gp24 Scaffolding protein
  • gp25 Decorating protein
  • gp26 Major capsid
KeywordsVIRAL PROTEIN / phage / bacteriophage / gene product 24 (gp24) / STRUCTURAL PROTEIN / gene product 25 (gp25) / scaffolding protein / decorating protein / major capsid protein / gene product 26 (gp26)
Function / homologyUncharacterised conserved protein UCP029215 / Uncharacterized protein conserved in bacteria (DUF2213) / : / Structural cement protein (E217 gp24/Pam3 gp6) / Virion protein / Capsid and scaffold protein / Capsid and scaffold protein
Function and homology information
Biological speciesPseudomonas virus Pa193
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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
A: gp26 Major capsid
B: gp26 Major capsid
C: gp26 Major capsid
D: gp26 Major capsid
E: gp26 Major capsid
K: gp25 Decorating protein
L: gp25 Decorating protein
M: gp25 Decorating protein
N: gp26 Major capsid
O: gp26 Major capsid
P: gp26 Major capsid
Q: gp26 Major capsid
R: gp26 Major capsid
S: gp26 Major capsid
G: gp24 Scaffolding protein
F: gp24 Scaffolding protein
H: gp24 Scaffolding protein
I: gp24 Scaffolding protein
J: gp24 Scaffolding protein


Theoretical massNumber of molelcules
Total (without water)782,29219
Polymers782,29219
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
gp26 Major capsid


Mass: 41610.918 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KVB7
#2: Protein gp25 Decorating protein


Mass: 21677.443 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5P1KV95
#3: Protein
gp24 Scaffolding protein


Mass: 51908.012 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa193 / References: UniProt: A0A5Q5ANU8
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
4RELION4.0.1CTF correction
9RELION4.0.1initial Euler assignment
10RELION4.0.1final Euler assignment
11RELION4.0.1classification
12RELION4.0.13D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 46075
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8278 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00533626
ELECTRON MICROSCOPYf_angle_d0.78745775
ELECTRON MICROSCOPYf_dihedral_angle_d4.6294636
ELECTRON MICROSCOPYf_chiral_restr0.055176
ELECTRON MICROSCOPYf_plane_restr0.0066008

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