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- EMDB-70396: S. griseus TUA bound UmbA4 complexes -

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Basic information

Entry
Database: EMDB / ID: EMD-70396
TitleS. griseus TUA bound UmbA4 complexes
Map data
Sample
  • Complex: Streptomyces griseus TUA bound Streptomyces coelicolor UmbA4 complex
    • Protein or peptide: Secreted esterase
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose
  • Ligand: 2,3-diacetamido-2,3-dideoxy-beta-D-mannopyranuronic acid
  • Ligand: 2,3-diacetamido-4-O-acetyl-2,3-dideoxy-beta-D-mannopyranuronic acid
KeywordsTeichuronic acid / UmbA4 / Umbrella toxin / Seattle structural genomics center for infectious disease / SSGCID / TOXIN
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
Biological speciesStreptomyces coelicolor (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPark YJ / Zhao Q / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio F / 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
DepositionApr 28, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70396.png

Downloads & links

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Map

FileDownload / File: emd_70396.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 280 pix.
= 280.56 Å		1 Å/pix.
x 280 pix.
= 280.56 Å		1 Å/pix.
x 280 pix.
= 280.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.002 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.0016284 - 2.7501922
Average (Standard dev.)0.005903831 (±0.08411909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 280.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70396_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #2

Fileemd_70396_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70396_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Streptomyces griseus TUA bound Streptomyces coelicolor UmbA4 complex

EntireName: Streptomyces griseus TUA bound Streptomyces coelicolor UmbA4 complex
Components
  • Complex: Streptomyces griseus TUA bound Streptomyces coelicolor UmbA4 complex
    • Protein or peptide: Secreted esterase
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose
  • Ligand: 2,3-diacetamido-2,3-dideoxy-beta-D-mannopyranuronic acid
  • Ligand: 2,3-diacetamido-4-O-acetyl-2,3-dideoxy-beta-D-mannopyranuronic acid

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Supramolecule #1: Streptomyces griseus TUA bound Streptomyces coelicolor UmbA4 complex

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

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Macromolecule #1: Secreted esterase

MacromoleculeName: Secreted esterase / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor (bacteria)
Molecular weightTheoretical: 73.207812 KDa
Recombinant expressionOrganism: Streptomyces coelicolor (bacteria)
SequenceString: ATGPAVTEGG HASTARLRIG DDQRACSGVL VAAQWLATAA SCFADDLGAG PVAAGKPQWR TTAVLGPAAG TTVEVVELVP RTDRDLVLA RLASPVAGTT PVPFATTAPA PGEELTVVGF GRTKEEWAPL TRHTAAFTVQ SVSGTTLALD GRTDDDAICA G DAGGPLLR ...String:
ATGPAVTEGG HASTARLRIG DDQRACSGVL VAAQWLATAA SCFADDLGAG PVAAGKPQWR TTAVLGPAAG TTVEVVELVP RTDRDLVLA RLASPVAGTT PVPFATTAPA PGEELTVVGF GRTKEEWAPL TRHTAAFTVQ SVSGTTLALD GRTDDDAICA G DAGGPLLR QKDGGFELVA LASQSWQGGC WGTDPAETRN DAVSPRLDNI AGGNTLTPGA VLRAEDSLVS NAARLTLRAD GD LVVVSNA GKTLWSTGTA GHLGATARFT DSGNLTVVDA DGTTVLWESA TTAPGGSAVL QDRGDLVVRD AQGASQWAAG TEV RHDYNG DGRSDMAAWY NYTDGRDAIH TFLGGTDGTL TKPLKSYDVA DGVWDTRAMK YLTGDFNGDG RGDTAVLKGY SDTS VKLWV ALGRADGGFD APYTAWSTPA GGFHISYMTP HAGDFNGDGR DDVAVWYAYA DGSTKLWTFT STDRGTFNAP FSSWS APSG SWLRSRVKSV VGDFDGDGRD DLSVFYGQGD DTVKTYVFPA APDGGFTTPA VWWQSASLDW NRTTPHAGDF NGDGRD DTL VWYDYPDGSD KTSTMLSERV SGKDRFGSAK VTLSSPPGNL DVTRMQFLTG DYDGDGRDDL ATLNHQADGT VKMWTWT AR PDAMFNGGIA GWSAPASSWV FGSAQFFTTY PKSGGGGSGG GGSKKKHHHH HHHH

UniProtKB: Secreted esterase

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Macromolecule #2: 2-acetamido-2-deoxy-alpha-D-galactopyranose

MacromoleculeName: 2-acetamido-2-deoxy-alpha-D-galactopyranose / type: ligand / ID: 2 / Number of copies: 30 / Formula: A2G
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-A2G:
2-acetamido-2-deoxy-alpha-D-galactopyranose

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Macromolecule #3: 2,3-diacetamido-2,3-dideoxy-beta-D-mannopyranuronic acid

MacromoleculeName: 2,3-diacetamido-2,3-dideoxy-beta-D-mannopyranuronic acid
type: ligand / ID: 3 / Number of copies: 25 / Formula: A1CAY
Molecular weightTheoretical: 276.243 Da

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Macromolecule #4: 2,3-diacetamido-4-O-acetyl-2,3-dideoxy-beta-D-mannopyranuronic acid

MacromoleculeName: 2,3-diacetamido-4-O-acetyl-2,3-dideoxy-beta-D-mannopyranuronic acid
type: ligand / ID: 4 / Number of copies: 5 / Formula: A1CAZ
Molecular weightTheoretical: 318.28 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 33.13 Å
Applied symmetry - Helical parameters - Δ&Phi: -151.14 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1182274
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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