8B3P | pdb_00008b3p

CryoEM structure of the round tip (proteins pVII/pVIII/pIX) from the f1 filamentous bacteriophage


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8B3P

This is version 1.1 of the entry. See complete history

Literature

Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly.

Conners, R.Leon-Quezada, R.I.McLaren, M.Bennett, N.J.Daum, B.Rakonjac, J.Gold, V.A.M.

(2023) Nat Commun 14: 2724-2724

  • DOI: https://doi.org/10.1038/s41467-023-37915-w
  • Primary Citation Related Structures: 
    8B3O, 8B3P, 8B3Q

  • PubMed Abstract: 

    Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.


  • Organizational Affiliation
    • Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.

Macromolecule Content 

  • Total Structure Weight: 270.83 kDa 
  • Atom Count: 17,620 
  • Modeled Residue Count: 2,370 
  • Deposited Residue Count: 2,575 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail virion protein G7PA [auth AAA],
HA [auth DDD],
L [auth BBB],
SA [auth EEE],
W [auth CCC]
33Enterobacteria phage f1Mutation(s): 0 
Gene Names: VII
Membrane Entity: Yes 
UniProt
Find proteins for P69534 (Enterobacteria phage f1)
Explore P69534 
Go to UniProtKB:  P69534
Entity Groups
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UniProt GroupP69534
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail virion protein G9PB [auth FFF],
IA [auth III],
M [auth GGG],
TA [auth JJJ],
X [auth HHH]
32Enterobacteria phage f1Mutation(s): 0 
Gene Names: IX
Membrane Entity: Yes 
UniProt
Find proteins for P69537 (Enterobacteria phage f1)
Explore P69537 
Go to UniProtKB:  P69537
Entity Groups
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UniProt GroupP69537
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein G8P50Enterobacteria phage f1Mutation(s): 1 
Gene Names: VIII
Membrane Entity: Yes 
UniProt
Find proteins for P69540 (Enterobacteria phage f1)
Explore P69540 
Go to UniProtKB:  P69540
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69540
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210363/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection