9H6A

Crystal structure of the E. coli F-plasmid VapBC toxin-antitoxin complex

• PDB DOI: https://doi.org/10.2210/pdb9H6A/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli KLY
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-24 Released: 2024-12-18 
• Deposition Author(s): Hollingshead, S., McVicker, G., Nielsen, M.R., Zhang, Y., Pilla, G., Jones, R.A., Thomas, J.C., Johansen, S.E.H., Exley, R.M., Brodersen, D.E., Tang, C.M.
• Funding Organization(s): Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.279 
• R-Value Work: 0.225 
• R-Value Observed: 0.231 

Starting Model: experimental

Literature

Shared mechanisms of enhanced plasmid maintenance and antibiotic tolerance mediated by the VapBC toxin:antitoxin system

Hollingshead, S., McVicker, G., Nielsen, M.R., Zhang, Y., Pilla, G., Jones, R.A., Thomas, J.C., Johansen, S.E.H., Exley, R.M., Brodersen, D.E., Tang, C.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 51.5 kDa 
• Atom Count: 3,138 
• Modelled Residue Count: 400 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA(fMet)-specific endonuclease VapC	A, C	132	Escherichia coli KLY	Mutation(s): 0  Gene Names: orf5, vapC, EWK56_24100, F7N46_24920, FGAF1022_52400, FGAS143_47190, G4A38_21190, G4A47_21040 EC: 3.1
UniProt
Find proteins for Q84A22 (Escherichia coli) Explore Q84A22  Go to UniProtKB:  Q84A22

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin	B, D	96	Escherichia coli KLY	Mutation(s): 0  Gene Names: orf6, vapB, ACN81_23035, FGAF1022_52390, FGAS143_47180, G4A38_21185, G4A47_21035
UniProt
Find proteins for Q7B3V0 (Escherichia coli) Explore Q7B3V0  Go to UniProtKB:  Q7B3V0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.279 
• R-Value Work: 0.225 
• R-Value Observed: 0.231 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.54	α = 90
b = 90.54	β = 90
c = 119.889	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Hollingshead, S., McVicker, G., Nielsen, M.R., Zhang, Y., Pilla, G., Jones, R.A., Thomas, J.C., Johansen, S.E.H., Exley, R.M., Brodersen, D.E., Tang, C.M.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	221924/Z/20/Z

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release