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- EMDB-73973: Streptomyces coelicolor UmbA4 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-73973
TitleStreptomyces coelicolor UmbA4 complex
Map data
Sample
  • Complex: Streptomyces coelicolor UmbA4 complex
    • Protein or peptide: UmbA4
KeywordsUmbA4 / Umbrella toxin / Seattle structural genomics center for infectious disease / SSGCID / TOXIN
Biological speciesStreptomyces coelicolor (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsPark YJ / Zhao Q / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Mougous JD / Veesler D
Funding support United States, 1 items
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
DepositionNov 19, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73973.png

Downloads & links

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Map

FileDownload / File: emd_73973.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 256 pix.
= 227.84 Å		0.89 Å/pix.
x 256 pix.
= 227.84 Å		0.89 Å/pix.
x 256 pix.
= 227.84 Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.2997889 - 0.5425748
Average (Standard dev.)0.00049738726 (±0.014900479)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 227.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_73973_additional_1.map
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Half map: #1

Fileemd_73973_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_73973_half_map_2.map
Projections & Slices
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Sample components

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Entire : Streptomyces coelicolor UmbA4 complex

EntireName: Streptomyces coelicolor UmbA4 complex
Components
  • Complex: Streptomyces coelicolor UmbA4 complex
    • Protein or peptide: UmbA4

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Supramolecule #1: Streptomyces coelicolor UmbA4 complex

SupramoleculeName: Streptomyces coelicolor UmbA4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces coelicolor (bacteria)

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Macromolecule #1: UmbA4

MacromoleculeName: UmbA4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor (bacteria)
Recombinant expressionOrganism: Streptomyces coelicolor (bacteria)
SequenceString: ATGPAVTEGG HASTARLRIG DDQRACSGVL VAAQWLATAA SCFADDLGAG PVAAGKPQWR TTAVLGPAAG TTVEVVELVP RTDRDLVLAR LASPVAGTTP VPFATTAPAP GEELTVVGFG RTKEEWAPLT RHTAAFTVQS VSGTTLALDG RTDDDAICAG DAGGPLLRQK ...String:
ATGPAVTEGG HASTARLRIG DDQRACSGVL VAAQWLATAA SCFADDLGAG PVAAGKPQWR TTAVLGPAAG TTVEVVELVP RTDRDLVLAR LASPVAGTTP VPFATTAPAP GEELTVVGFG RTKEEWAPLT RHTAAFTVQS VSGTTLALDG RTDDDAICAG DAGGPLLRQK DGGFELVALA SQSWQGGCWG TDPAETRNDA VSPRLDNIAG GNTLTPGAVL RAEDSLVSNA ARLTLRADGD LVVVSNAGKT LWSTGTAGHL GATARFTDSG NLTVVDADGT TVLWESATTA PGGSAVLQDR GDLVVRDAQG ASQWAAGTEV RHDYNGDGRS DMAAWYNYTD GRDAIHTFLG GTDGTLTKPL KSYDVADGVW DTRAMKYLTG DFNGDGRGDT AVLKGYSDTS VKLWVALGRA DGGFDAPYTA WSTPAGGFHI SYMTPHAGDF NGDGRDDVAV WYAYADGSTK LWTFTSTDRG TFNAPFSSWS APSGSWLRSR VKSVVGDFDG DGRDDLSVFY GQGDDTVKTY VFPAAPDGGF TTPAVWWQSA SLDWNRTTPH AGDFNGDGRD DTLVWYDYPD GSDKTSTMLS ERVSGKDRFG SAKVTLSSPP GNLDVTRMQF LTGDYDGDGR DDLATLNHQA DGTVKMWTWT ARPDAMFNGG IAGWSAPASS WVFGSAQFFT TYPKSGGGGS GGGGSKKKHH HHHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 200137
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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