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- PDB-9oee: S. griseus TUA bound UmbA4 complexes -

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Basic information

Entry
Database: PDB / ID: 9oee
TitleS. griseus TUA bound UmbA4 complexes
ComponentsSecreted esterase
KeywordsTOXIN / Teichuronic acid / UmbA4 / Umbrella toxin / Seattle structural genomics center for infectious disease / SSGCID
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
T-cell immunomodulatory protein / FG-GAP-like repeat / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / FG-GAP repeat / Integrin alpha, N-terminal / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. ...T-cell immunomodulatory protein / FG-GAP-like repeat / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / : / 2-acetamido-2-deoxy-alpha-D-galactopyranose / Secreted esterase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 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: Cell / Year: 2025
Title: The unique architecture of umbrella toxins permits a two-tiered molecular bet-hedging strategy for interbacterial antagonism.
Authors: Qinqin Zhao / Jiri Vlach / Young-Jun Park / Yongjun Tan / Savannah K Bertolli / Pooja Srinivas / Pinyu Liao / Connor R Fitzpatrick / Jeffery L Dangl / Parastoo Azadi / Frank DiMaio / S Brook ...Authors: Qinqin Zhao / Jiri Vlach / Young-Jun Park / Yongjun Tan / Savannah K Bertolli / Pooja Srinivas / Pinyu Liao / Connor R Fitzpatrick / Jeffery L Dangl / Parastoo Azadi / Frank DiMaio / S Brook Peterson / Dapeng Zhang / David Veesler / Joseph D Mougous /
Abstract: Bacteria exist in competitive and rapidly changing environments in which the nature of future threats cannot be easily predicted. Streptomyces coelicolor produces three antibacterial umbrella ...Bacteria exist in competitive and rapidly changing environments in which the nature of future threats cannot be easily predicted. Streptomyces coelicolor produces three antibacterial umbrella particles that harbor distinct polymorphic toxin domains and an overlapping set of six diversified lectins. Here, we show that the exquisite specificity of umbrella particles derives from lectin-mediated species-specific binding to previously undescribed hypervariable surface glycoconjugates. A cryo-electron microscopy (cryo-EM) structure of one such lectin in complex with its oligosaccharide substrate defines the molecular basis for targeting through the coordinated recognition of multiple glycan features. Biochemical and genetic studies of several target species, in conjunction with lectin-swapping experiments, support a model whereby S. coelicolor umbrella toxin diversification at the levels of lectin composition and toxin polymorphism represents a unique, two-tiered bet-hedging strategy. Bioinformatic analyses support this as a means by which the unusual architecture of umbrella toxins offers Streptomyces a generalizable strategy to antagonize an unpredictable array of competitors.
History
DepositionApr 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted esterase
B: Secreted esterase
D: Secreted esterase
F: Secreted esterase
H: Secreted esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,17365
Polymers366,0395
Non-polymers15,13460
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Secreted esterase


Mass: 73207.812 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Production host: Streptomyces coelicolor (bacteria) / References: UniProt: Q93J50
#2: Sugar...
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical...
ChemComp-A1CAY / 2,3-diacetamido-2,3-dideoxy-beta-D-mannopyranuronic acid


Mass: 276.243 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C10H16N2O7
#4: Chemical
ChemComp-A1CAZ / 2,3-diacetamido-4-O-acetyl-2,3-dideoxy-beta-D-mannopyranuronic acid


Mass: 318.280 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H18N2O8
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Streptomyces griseus TUA bound Streptomyces coelicolor UmbA4 complex
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Streptomyces coelicolor (bacteria)
Source (recombinant)Organism: Streptomyces coelicolor (bacteria)
Buffer solutionpH: 7
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: TFS 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: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -151.14 ° / Axial rise/subunit: 33.13 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1182274 / Symmetry type: HELICAL

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