6GIG

Structural insights into AapA1 toxin

• PDB DOI: https://doi.org/10.2210/pdb6GIG/pdb
• BMRB: 34271

• Classification: ANTITOXIN
• Organism(s): Helicobacter pylori
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2018-05-11 Released: 2019-09-11 
• Deposition Author(s): Salgado, G.F., Korkut, D.N.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structural insights into the AapA1 toxin of Helicobacter pylori.

Korkut, D.N., Alves, I.D., Vogel, A., Chabas, S., Sharma, C.M., Martinez, D., Loquet, A., Salgado, G.F., Darfeuille, F.

(2020) Biochim Biophys Acta Gen Subj 1864: 129423-129423

• PubMed: 31476357 
• DOI: https://doi.org/10.1016/j.bbagen.2019.129423
• Primary Citation of Related Structures:  
  6GIF, 6GIG


• PubMed Abstract: 
  

  We previously reported the identification of the aapA1/IsoA1 locus as part of a new family of toxin-antitoxin (TA) systems in the human pathogen Helicobacter pylori. AapA1 belongs to type I TA bacterial toxins, and both its mechanism of action towards the membrane and toxicity features are still unclear.

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Organizational Affiliation: 

INSERM, U1212, CNRS UMR 5320, Univ. Bordeaux, Laboratoire ARNA, F-33076 Bordeaux, France; Univ. Bordeaux, IECB, Laboratoire ARNA, F-33600 Pessac, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 3.47 kDa 
• Atom Count: 243 
• Modelled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AapA1	A	30	Helicobacter pylori	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0DUM4 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P0DUM4  Go to UniProtKB:  P0DUM4

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Salgado, G.F., Korkut, D.N.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-12-BSV5-0025

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other