8G1R | pdb_00008g1r

A Vibrio cholerae viral satellite enables efficient horizontal transfer by using an external scaffold to assemble hijacked coat proteins into small capsids


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

A Vibrio cholerae viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids.

Boyd, C.M.Subramanian, S.Dunham, D.T.Parent, K.N.Seed, K.D.

(2023) bioRxiv 

  • DOI: https://doi.org/10.1101/2023.03.01.530633
  • Primary Citation Related Structures: 
    8G1R

  • PubMed Abstract: 

    Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a satellite from Vibrio cholerae , PLE, remodels the capsid it has been predicted to steal from the phage ICP1 (1). We identified that a PLE-encoded protein, TcaP, is both necessary and sufficient to form small capsids during ICP1 infection. Interestingly, we found that PLE is dependent on small capsids for efficient transduction of its genome, making it the first satellite to have this requirement. ICP1 isolates that escaped TcaP-mediated remodeling acquired substitutions in the coat protein, suggesting an interaction between these two proteins. With a procapsid-like-particle (PLP) assembly platform in Escherichia coli , we demonstrated that TcaP is a bona fide scaffold that regulates the assembly of small capsids. Further, we studied the structure of PLE PLPs using cryogenic electron microscopy and found that TcaP is an external scaffold, that is functionally and somewhat structurally similar to the external scaffold, Sid, encoded by the unrelated satellite P4 (2). Finally, we showed that TcaP is largely conserved across PLEs. Together, these data support a model in which TcaP directs the assembly of small capsids comprised of ICP1 coat proteins, which inhibits the complete packaging of the ICP1 genome and permits more efficient packaging of replicated PLE genomes.


  • Organizational Affiliation
    • Department of Plant and Microbial Biology, Seed Lab, University of California - Berkeley, CA 94720.

Macromolecule Content 

  • Total Structure Weight: 186.94 kDa 
  • Atom Count: 9,889 
  • Modeled Residue Count: 1,457 
  • Deposited Residue Count: 1,678 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
major head protein
A, B, C, D
345Vibrio phage ICP1_2011_AMutation(s): 0 
Gene Names: ICP12011A_121
UniProt
Find proteins for A0ACD6B928 (Vibrio phage ICP1_2011_A)
Explore A0ACD6B928 
Go to UniProtKB:  A0ACD6B928
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B928
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine protease298Vibrio choleraeMutation(s): 0 
UniProt
Find proteins for M1R2Y9 (Vibrio cholerae serotype O1 biovar El Tor)
Explore M1R2Y9 
Go to UniProtKB:  M1R2Y9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1R2Y9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110185
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM116789
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140803
National Science Foundation (NSF, United States)United States1750125
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI127652
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI127652

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary