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- PDB-9jg9: Structure of the BtpeA effector and BtaeB effector bound to the V... -

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Basic information

Entry
Database: PDB / ID: 9jg9
TitleStructure of the BtpeA effector and BtaeB effector bound to the VgrG spike from the Type VI secretion system
Components
  • 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 / DUF3289 family protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 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: To Be Published
Title: Synergistic Function and Effector-Dependent Secretion in the Type VI Secretion System
Authors: Li, W.X. / Zheng, S.N. / Chen, Z. / Gao, X.
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
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)342,2856
Polymers342,2195
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 / BtpeA (Bacteroides T6SS Phosphatase Effector A)


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 / BtaeB (Bacteroides T6SS Amidase Effector B)


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 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
#4: 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 complex / Type: COMPLEX / Entity ID: #1-#3 / 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: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73616 / Symmetry type: POINT
Atomic model buildingB value: 112.3 / Protocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE

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