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- PDB-8w22: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF... -

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Basic information

Entry
Database: PDB / ID: 8w22
TitleUmb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)
Components
  • Intein C-terminal splicing domain-containing protein
  • Secreted esterase
  • Secreted protein
KeywordsTOXIN / Streptomyces / Umbrella toxin particles / Alanine leucine phenylalanine-rich (ALF) repeat proteins / Seattle structural genomics center for infectious disease / SSGCID
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Protein of unknown function DUF312, ALF / Short repeats of unknown function / Pretoxin HINT domain / Double-stranded DNA deaminase toxin A / Double-stranded DNA deaminase toxin A / : / FG-GAP-like repeat / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain N-terminal ...Protein of unknown function DUF312, ALF / Short repeats of unknown function / Pretoxin HINT domain / Double-stranded DNA deaminase toxin A / Double-stranded DNA deaminase toxin A / : / FG-GAP-like repeat / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / FG-GAP repeat / Integrin alpha, N-terminal / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Intein C-terminal splicing domain-containing protein / Secreted protein / Secreted esterase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsPark, Y.J. / Zhao, Q. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio, F. / Mougous, J.D. / Veesler, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: Nature / Year: 2024
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.
History
DepositionFeb 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intein C-terminal splicing domain-containing protein
B: Secreted protein
C: Secreted esterase


Theoretical massNumber of molelcules
Total (without water)214,3403
Polymers214,3403
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Intein C-terminal splicing domain-containing 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) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV2
#2: Protein Secreted protein


Mass: 17186.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV3
#3: Protein Secreted esterase


Mass: 54437.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: endogenous tags to purified the complex from natural source
Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386275 / Symmetry type: POINT

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