9JG9 | pdb_00009jg9

Structure of the BtpeA effector and BtaeB effector bound to the VgrG spike from the Type VI secretion system

• PDB DOI: https://doi.org/10.2210/pdb9JG9/pdb
• EM Map EMD-61459: EMDB EMDataResource

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Bacteroides fragilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-06 Released: 2025-09-10 
• Deposition Author(s): Zheng, S.N., Li, W.X., Chen, Z., Gao, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Synergistic Function and Effector-Dependent Secretion in the Type VI Secretion System

Li, W.X., Zheng, S.N., Chen, Z., Gao, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 342.28 kDa 
• Atom Count: 14,506 
• Modeled Residue Count: 1,880 
• Deposited Residue Count: 3,079 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3289 family protein	A [auth B]	608	Bacteroides fragilis	Mutation(s): 0  Gene Names: FSA06_12460
UniProt
Find proteins for A0A5C6JKA9 (Bacteroides fragilis) Explore A0A5C6JKA9  Go to UniProtKB:  A0A5C6JKA9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase C39-like domain-containing protein	B [auth C]	617	Bacteroides fragilis	Mutation(s): 0  Gene Names: FSA06_12440

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Type VI secretion system spike protein VgrG	C [auth E], D [auth F], E [auth G]	618	Bacteroides fragilis	Mutation(s): 0  Gene Names: FSA06_12470
UniProt
Find proteins for A0A5C6HF51 (Bacteroides fragilis) Explore A0A5C6HF51  Go to UniProtKB:  A0A5C6HF51

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Zheng, S.N., Li, W.X., Chen, Z., Gao, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	323B2003

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release