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Open data
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Basic information
Entry | Database: PDB / ID: 8w20 | ||||||
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Title | Umb1 umbrella toxin particle | ||||||
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Function / homology | ![]() | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, Y.J. / Zhao, Q. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio, F. / Mougous, J.D. / Veesler, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Streptomyces umbrella toxin particles block hyphal growth of competing species. Authors: Qinqin Zhao / Savannah Bertolli / Young-Jun Park / Yongjun Tan / Kevin J Cutler / Pooja Srinivas / Kyle L Asfahl / Citlali Fonesca-García / Larry A Gallagher / Yaqiao Li / Yaxi Wang / Devin ...Authors: Qinqin Zhao / Savannah Bertolli / Young-Jun Park / Yongjun Tan / Kevin J Cutler / Pooja Srinivas / Kyle L Asfahl / Citlali Fonesca-García / Larry A Gallagher / Yaqiao Li / Yaxi Wang / Devin Coleman-Derr / Frank DiMaio / Dapeng Zhang / S Brook Peterson / David Veesler / Joseph D Mougous / ![]() Abstract: Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive. The production of these antibacterial molecules reflects the relentless ...Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species. 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. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 452.7 KB | Display | ![]() |
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PDB format | ![]() | 320.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 43736MC ![]() 8w22C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | ![]() Mass: 17186.270 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 54437.102 Da / Num. of mol.: 5 / Source method: isolated from a natural source Details: endogenous tags to purified the complex from natural source Source: (natural) ![]() ![]() #3: Protein | | Mass: 142716.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: endogenous tags to purified the complex from natural source Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Umb1 umbrella toxin particle / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction![]() | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386275 / Symmetry type: POINT |