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- PDB-9vnd: Structure of the Bacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 Het... -

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Basic information

Entry
Database: PDB / ID: 9vnd
TitleStructure of the Bacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 Heterohexamer in Complex with the Effector Bte1
Components
  • Bacteroides fragilis NCTC9343 T6SS Hcp2
  • Bacteroides fragilis NCTC9343 T6SS Hcp3
  • Bacteroides fragilis NCTC9343 T6SS V1 effector Bte1
KeywordsSTRUCTURAL PROTEIN / Bacteroides fragilis / T6SS / Hcp / effector
Function / homologyHemolysin coregulated protein (Hcp) TssD / Hemolysin coregulated protein Hcp (TssD) / type VI protein secretion system complex / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZheng, S.N. / Chen, Z. / Li, W.X. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)323B2003 China
CitationJournal: Nat Commun / Year: 2026
Title: Conformational selection enables effector-specific delivery by Hcp heterohexamers in gut symbionts
Authors: Zheng, S.N. / Li, W.X. / Gao, X.
History
DepositionJun 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data 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: Bacteroides fragilis NCTC9343 T6SS Hcp3
C: Bacteroides fragilis NCTC9343 T6SS Hcp2
A: Bacteroides fragilis NCTC9343 T6SS Hcp2
D: Bacteroides fragilis NCTC9343 T6SS Hcp2
J: Bacteroides fragilis NCTC9343 T6SS V1 effector Bte1
E: Bacteroides fragilis NCTC9343 T6SS Hcp3
F: Bacteroides fragilis NCTC9343 T6SS Hcp2


Theoretical massNumber of molelcules
Total (without water)128,1077
Polymers128,1077
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Bacteroides fragilis NCTC9343 T6SS Hcp3


Mass: 15389.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: BF9343_1938 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A380Z0E1
#2: Protein
Bacteroides fragilis NCTC9343 T6SS Hcp2


Mass: 16112.126 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: BF9343_1939 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LDT5
#3: Protein Bacteroides fragilis NCTC9343 T6SS V1 effector Bte1


Mass: 32879.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: BF9343_1937 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LDT7
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: Structure of the Bacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 Heterohexamer in Complex with the Effector Bte1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacteroides fragilis NCTC 9343 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.35 mg/ml / Embedding 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: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
12RELION3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60133 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023745
ELECTRON MICROSCOPYf_angle_d0.5685030
ELECTRON MICROSCOPYf_dihedral_angle_d4.444468
ELECTRON MICROSCOPYf_chiral_restr0.044580
ELECTRON MICROSCOPYf_plane_restr0.004604

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