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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9JG9

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5C6JKA9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5C6HF51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.