8I4M

Portal-tail complex structure of the Cyanophage P-SCSP1u

  • Classification: VIRUS
  • Organism(s): Prochlorococcus phage P-SCSP1u
  • Mutation(s): No 

  • Deposited: 2023-01-19 Released: 2023-11-01 
  • Deposition Author(s): Liu, H., Dang, S.
  • Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses.

Cai, L.Liu, H.Zhang, W.Xiao, S.Zeng, Q.Dang, S.

(2023) Nat Commun 14: 6438-6438

  • DOI: https://doi.org/10.1038/s41467-023-42258-7
  • Primary Citation of Related Structures:  
    8I4L, 8I4M

  • PubMed Abstract: 

    Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria Podovirus clade C) cyanophages, belonging to the T7-like podoviruses, contain the smallest genomes among cyanopodoviruses and exhibit distinct infection kinetics. However, understanding of the MPP-C cyanophage infection process is hindered by the lack of high-resolution structural information. Here, we report the cryo-EM structure of the cyanophage P-SCSP1u, a representative member of the MPP-C phages, in its native form at near-atomic resolution, which reveals the assembly mechanism of the capsid and molecular interaction of the portal-tail complex. Structural comparison of the capsid proteins of P-SCSP1u and other podoviruses with known structures provides insights into the evolution of T7-like viruses. Furthermore, our study provides the near-atomic resolution structure of portal-tail complex for T7-like viruses. On the basis of previously reported structures of phage T7, we identify an additional valve and gate to explain the DNA gating mechanism for the T7-like viruses.


  • Organizational Affiliation

    Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein(gp 16) of the cyanophage P-SCSP1u565Prochlorococcus phage P-SCSP1uMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nozzle protein(gp 23) of the cyanophage P-SCSP1u806Prochlorococcus phage P-SCSP1uMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Adaptor protein(gp22) of the cyanophage P-SCSP1u200Prochlorococcus phage P-SCSP1uMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fiber protein(gp 28) of the cyanophage P-SCSP1u1,079Prochlorococcus phage P-SCSP1uMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.15

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Database references