8C2Q | pdb_00008c2q

Silver ion-bound structure of the silver specific chaperone SilF needed for bacterial silver resistance


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 8C2Q

This is version 1.0 of the entry. See complete history

Literature

The battle for silver binding: How the interplay between the SilE, SilF, and SilB proteins contributes to the silver efflux pump mechanism.

Arrault, C.Monneau, Y.R.Martin, M.Cantrelle, F.X.Boll, E.Chirot, F.Comby Zerbino, C.Walker, O.Hologne, M.

(2023) J Biological Chem 299: 105004-105004

  • DOI: https://doi.org/10.1016/j.jbc.2023.105004
  • Primary Citation Related Structures: 
    8BXJ, 8C2Q

  • PubMed Abstract: 

    The resistance of gram-negative bacteria to silver ions is mediated by a silver efflux pump, which mainly relies on a tripartite efflux complex SilCBA, a metallochaperone SilF and an intrinsically disordered protein SilE. However, the precise mechanism by which silver ions are extruded from the cell and the different roles of SilB, SilF, and SilE remain poorly understood. To address these questions, we employed nuclear magnetic resonance and mass spectrometry to investigate the interplay between these proteins. We first solved the solution structures of SilF in its free and Ag + -bound forms, and we demonstrated that SilB exhibits two silver binding sites in its N and C termini. Conversely to the homologous Cus system, we determined that SilF and SilB interact without the presence of silver ions and that the rate of silver dissociation is eight times faster when SilF is bound to SilB, indicating the formation of a SilF-Ag-SilB intermediate complex. Finally, we have shown that SilE does not bind to either SilF or SilB, regardless of the presence or absence of silver ions, further corroborating that it merely acts as a regulator that prevents the cell from being overloaded with silver. Collectively, we have provided further insights into protein interactions within the sil system that contribute to bacterial resistance to silver ions.


  • Organizational Affiliation
    • Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, Villeurbanne, France.

Macromolecule Content 

  • Total Structure Weight: 10.82 kDa 
  • Atom Count: 749 
  • Modeled Residue Count: 100 
  • Deposited Residue Count: 100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Copper ABC transporter substrate-binding protein100Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: ORF96
UniProt
Find proteins for Q9ZHD1 (Salmonella typhimurium)
Explore Q9ZHD1 
Go to UniProtKB:  Q9ZHD1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZHD1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AG
(Subject of Investigation/LOI)

Query on AG



Download:Ideal Coordinates CCD File
B [auth A]SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release