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- PDB-9jg8: Structure of cargo complex (BtpeA-BtaeB-BtapC) bound to the VgrG ... -

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Basic information

Entry
Database: PDB / ID: 9jg8
TitleStructure of cargo complex (BtpeA-BtaeB-BtapC) bound to the VgrG spike from the Type VI secretion system
Components
  • Bacteroides T6SS Adapter Protein C
  • DUF3289 family protein
  • Peptidase C39-like domain-containing protein
  • Type VI secretion system spike protein VgrG
KeywordsANTIMICROBIAL PROTEIN / T6SS / Co-delivery / effector complex / VgrG spike
Function / homology
Function and homology information


Conserved hypothetical protein CHP03034 / Protein of unknown function DUF4280 / Protein of unknown function (DUF3289) / Domain of unknown function (DUF4280) / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
: / Phage baseplate assembly protein V / Uncharacterized protein / DUF3289 family protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsZheng, S.N. / Li, W.X. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)323B2003 China
CitationJournal: Cell Host Microbe / Year: 2025
Title: A conserved adaptor orchestrates co-secretion of synergistic type VI effectors in gut Bacteroidota.
Authors: Weixun Li / Shuaining Zheng / Xiaoning Xu / Jing He / Xuyao Jiao / Mingyu Wang / Wei Hu / Shengying Li / Xianzhi Jiang / Bentley Lim / Feng Shao / Xiang Gao /
Abstract: Interbacterial competition is crucial for shaping microbial communities and is often mediated by type VI secretion systems (T6SSs) that inject effectors into competing bacteria. T6SS effectors are ...Interbacterial competition is crucial for shaping microbial communities and is often mediated by type VI secretion systems (T6SSs) that inject effectors into competing bacteria. T6SS effectors are released via structural proteins such as VgrG, but the secretion timing and coordination are unclear. Here, we report two effectors, BtpeA (Bacteroides T6SS phosphatase effector A) and BtaeB (Bacteroides T6SS amidase effector B), within the Bacteroidota T6SS that exert distinct cell-wall destructive activities critical for interspecies competition but whose secretion is interdependent. BtpeA and BtaeB co-secretion requires an adaptor protein, BtapC (Bacteroides T6SS adaptor protein C), that mediates the sequential assembly of the pre-firing complex, VgrG-BtpeA-BtaeB-BtapC. Structural analyses of this quaternary complex elucidate multi-cargo loading mechanisms with a conserved loop in BtaeB serving as a "checkpoint" to ensure BtpeA co-secretion. During mouse colonization, the combined activities of BtpeA and BtaeB significantly exceed the sum of the individual effectors. These findings unveil a T6SS-mediated co-delivery mechanism that ensures functional synergism of effectors, highlighting potential applications in modulating gut microbiota.
History
DepositionSep 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DUF3289 family protein
C: Peptidase C39-like domain-containing protein
A: Bacteroides T6SS Adapter Protein C
G: Type VI secretion system spike protein VgrG
E: Type VI secretion system spike protein VgrG
F: Type VI secretion system spike protein VgrG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,1237
Polymers372,0576
Non-polymers651
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 DUF3289 family protein


Mass: 68774.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12460 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6JKA9
#2: Protein Peptidase C39-like domain-containing protein


Mass: 69103.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12440 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6HES3
#3: Protein Bacteroides T6SS Adapter Protein C


Mass: 29837.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6HF83
#4: Protein Type VI secretion system spike protein VgrG


Mass: 68113.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6HF51
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: VgrG-BtpeA-BtaeB-BtapC quaternary complex / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Bacteroides fragilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106021 / Symmetry type: POINT
RefinementCross valid method: NONE

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