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- EMDB-64503: Bacteroides fragilis T6SS effector-immunity BteO-BtiO complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64503
TitleBacteroides fragilis T6SS effector-immunity BteO-BtiO complex
Map data
Sample
  • Complex: Bacteroides fragilis T6SS effector-immunity BteO-BtiO complex
KeywordsBacteroides fragilis T6SS effector-immunity protein / TOXIN
Biological speciesBacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsHe J / Gao X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: A nonenzymatic effector disrupts cell wall homeostasis via OmpA targeting to mediate interbacterial competition.
Authors: Jing He / Zhe Chen / Kun Jiang / Yan Yang / Weixun Li / Xiaotong Wang / Xiaoning Xu / Shuaining Zheng / Xuyao Jiao / Xudong Chen / Liujie Huo / Bentley Lim / Shuang-Jiang Liu / Xiang Gao /
Abstract: The human gut microbiome is a dynamic ecosystem where bacteria engage in interspecies competition using molecular weapons such as the type VI secretion system (T6SS). Here, we characterize BteO-BtiO, ...The human gut microbiome is a dynamic ecosystem where bacteria engage in interspecies competition using molecular weapons such as the type VI secretion system (T6SS). Here, we characterize BteO-BtiO, a unique effector-immunity pair in that mediates antagonism via a nonenzymatic mechanism. Microscopy reveals that BteO exposure leads to cell elongation, membrane blebbing, and lysis in sensitive strains. Structural and biochemical analyses demonstrate that BteO disrupts cell wall homeostasis by binding to conserved C-terminal domains of OmpA-family proteins (OmpAs), which are critical for outer membrane integrity. The immunity protein BtiO neutralizes BteO by mimicking the OmpA-binding interface. We further show that bile salts enhance BteO-mediated killing in vitro and that BteO confers a competitive advantage in the mammalian gut. Remarkably, BteO exhibits broad-spectrum activity across species. These findings reveal a nonenzymatic strategy of bacterial antagonism and broaden our understanding of T6SS effector diversity within .
History
DepositionMay 5, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64503.png

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Map

FileDownload / File: emd_64503.map.gz / Format: CCP4 / Size: 48.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 234 pix.
= 248.04 Å		1.06 Å/pix.
x 234 pix.
= 248.04 Å		1.06 Å/pix.
x 234 pix.
= 248.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.4717151 - 0.7645243
Average (Standard dev.)-0.00044371453 (±0.023922434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions234234234
Spacing234234234
CellA=B=C: 248.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64503_half_map_1.map
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Half map: #2

Fileemd_64503_half_map_2.map
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Sample components

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Entire : Bacteroides fragilis T6SS effector-immunity BteO-BtiO complex

EntireName: Bacteroides fragilis T6SS effector-immunity BteO-BtiO complex
Components
  • Complex: Bacteroides fragilis T6SS effector-immunity BteO-BtiO complex

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Supramolecule #1: Bacteroides fragilis T6SS effector-immunity BteO-BtiO complex

SupramoleculeName: Bacteroides fragilis T6SS effector-immunity BteO-BtiO complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacteroides fragilis (bacteria)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43438
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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