8W22 | pdb_00008w22

Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8W22

This is version 1.3 of the entry. See complete history

Literature

Streptomyces umbrella toxin particles block hyphal growth of competing species.

Zhao, Q.Bertolli, S.Park, Y.J.Tan, Y.Cutler, K.J.Srinivas, P.Asfahl, K.L.Fonesca-Garcia, C.Gallagher, L.A.Li, Y.Wang, Y.Coleman-Derr, D.DiMaio, F.Zhang, D.Peterson, S.B.Veesler, D.Mougous, J.D.

(2024) Nature 629: 165-173

  • DOI: https://doi.org/10.1038/s41586-024-07298-z
  • Primary Citation Related Structures: 
    8W20, 8W22

  • PubMed Abstract: 

    Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive 1 . The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species 1,2 . Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly 3,4 . Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.


  • Organizational Affiliation
    • Department of Microbiology, University of Washington, Seattle, WA, USA.

Macromolecule Content 

  • Total Structure Weight: 214.34 kDa 
  • Atom Count: 3,750 
  • Modeled Residue Count: 629 
  • Deposited Residue Count: 2,049 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Intein C-terminal splicing domain-containing protein1,368Streptomyces coelicolor A3(2)Mutation(s): 0 
UniProt
Find proteins for Q9ACV2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9ACV2 
Go to UniProtKB:  Q9ACV2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ACV2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Secreted protein166Streptomyces coelicolor A3(2)Mutation(s): 0 
UniProt
Find proteins for Q9ACV3 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9ACV3 
Go to UniProtKB:  Q9ACV3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ACV3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Secreted esterase515Streptomyces coelicolor A3(2)Mutation(s): 0 
UniProt
Find proteins for Q9ACV4 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9ACV4 
Go to UniProtKB:  Q9ACV4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ACV4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00036

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary