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 8HDR | pdb_00008hdr

Cyanophage Pam3 neck


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Fine structure and assembly pattern of a minimal myophage Pam3.

Yang, F., Jiang, Y.L., Zhang, J.T., Zhu, J., Du, K., Yu, R.C., Wei, Z.L., Kong, W.W., Cui, N., Li, W.F., Chen, Y., Li, Q., Zhou, C.Z.

(2023) Proc Natl Acad Sci U S A 120: e2213727120-e2213727120

  • DOI: https://doi.org/10.1073/pnas.2213727120
  • Primary Citation Related Structures: 
    7YFW, 7YFZ, 8HDR, 8HDS, 8HDT, 8HDW

  • PubMed Abstract: 

    The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater Myoviridae cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.


  • Organizational Affiliation: 
    • School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.

Macromolecule Content 

  • Total Structure Weight: 1,122.95 kDa 
  • Atom Count: 78,708 
  • Modeled Residue Count: 10,296 
  • Deposited Residue Count: 10,332 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
pam3 tube protein142uncultured cyanophageMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Pam3 connector protein110uncultured cyanophageMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Pam3 terminator protein156uncultured cyanophageMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Pam3 sheath protein384uncultured cyanophageMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Pam3 adaptor protein131uncultured cyanophageMutation(s): 0 
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFA0903100

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection