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- PDB-9jdh: Crystal structure of the T6SS effector BtaeB-NTD from Bacteroides... -

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Basic information

Entry
Database: PDB / ID: 9jdh
TitleCrystal structure of the T6SS effector BtaeB-NTD from Bacteroides fragilis
ComponentsPeptidase C39-like domain-containing protein
KeywordsANTIMICROBIAL PROTEIN / Bacteroides fragilis / T6SS / effector / Interbacterial antagonism
Function / homologyDI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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
DepositionAug 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase C39-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3915
Polymers43,9661
Non-polymers4244
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.670, 49.370, 183.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Peptidase C39-like domain-containing protein


Mass: 43966.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BtaeB N-terminal domain of the T6ss effector of Bacteroides fragilis.
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12440 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6HES3
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium acetate (PH=5.2), 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.18→91.88 Å / Num. obs: 21523 / % possible obs: 99.73 % / Redundancy: 12.2 % / Biso Wilson estimate: 38.45 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.7
Reflection shellResolution: 2.18→2.26 Å / Num. unique obs: 2083 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot1.20.1_4487model building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→91.88 Å / SU ML: 0.2885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2482 1066 4.95 %
Rwork0.1999 20453 -
obs0.2023 21519 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.4 Å2
Refinement stepCycle: LAST / Resolution: 2.18→91.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 28 141 3185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273097
X-RAY DIFFRACTIONf_angle_d0.57544162
X-RAY DIFFRACTIONf_chiral_restr0.0489464
X-RAY DIFFRACTIONf_plane_restr0.0042530
X-RAY DIFFRACTIONf_dihedral_angle_d16.91461174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.280.31871260.24362499X-RAY DIFFRACTION99.62
2.28-2.40.28881300.21572494X-RAY DIFFRACTION99.89
2.4-2.550.26111270.22352533X-RAY DIFFRACTION99.89
2.55-2.750.28641260.22422560X-RAY DIFFRACTION99.85
2.75-3.020.24461370.21012503X-RAY DIFFRACTION99.96
3.02-3.460.26121500.20272550X-RAY DIFFRACTION99.93
3.46-4.360.23451530.17822581X-RAY DIFFRACTION99.78
4.36-91.880.21841170.19222733X-RAY DIFFRACTION99.03

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