9B40 | pdb_00009b40

Pseudomonas phage Pa193 5-fold vertex (capsid, decorating, and scaffolding proteins)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM analysis of Pseudomonas phage Pa193 structural components.

Iglesias, S.M.Hou, C.D.Reid, J.Schauer, E.Geier, R.Soriaga, A.Sim, L.Gao, L.Whitelegge, J.Kyme, P.Birx, D.Lemire, S.Cingolani, G.

(2024) Commun Biol 7: 1275-1275

  • DOI: https://doi.org/10.1038/s42003-024-06985-x
  • Primary Citation of Related Structures:  
    9B40, 9B41, 9B42, 9B45

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
gp26 Major capsid382Pseudomonas virus Pa193Mutation(s): 0 
UniProt
Find proteins for A0A5P1KVB7 (Pseudomonas virus Pa193)
Explore A0A5P1KVB7 
Go to UniProtKB:  A0A5P1KVB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P1KVB7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
gp25 Decorating proteinF [auth K],
G [auth L],
H [auth M]
211Pseudomonas virus Pa193Mutation(s): 0 
UniProt
Find proteins for A0A5P1KV95 (Pseudomonas virus Pa193)
Explore A0A5P1KV95 
Go to UniProtKB:  A0A5P1KV95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P1KV95
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
gp24 Scaffolding proteinO [auth G],
P [auth F],
Q [auth H],
R [auth I],
S [auth J]
478Pseudomonas virus Pa193Mutation(s): 0 
UniProt
Find proteins for A0A5Q5ANU8 (Pseudomonas virus Pa193)
Explore A0A5Q5ANU8 
Go to UniProtKB:  A0A5Q5ANU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5Q5ANU8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0.1
MODEL REFINEMENTPHENIX1.21

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM140733

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release