3QG6 | pdb_00003qg6

Structural Basis for Ligand Recognition and Discrimination of a Quorum Quenching Antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.239 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3QG6

This is version 1.4 of the entry. See complete history

Literature

Structural Basis for Ligand Recognition and Discrimination of a Quorum-quenching Antibody.

Kirchdoerfer, R.N.Garner, A.L.Flack, C.E.Mee, J.M.Horswill, A.R.Janda, K.D.Kaufmann, G.F.Wilson, I.A.

(2011) J Biological Chem 286: 17351-17358

  • DOI: https://doi.org/10.1074/jbc.M111.231258
  • Primary Citation Related Structures: 
    3QG6, 3QG7

  • PubMed Abstract: 

    In the postantibiotic era, available treatment options for severe bacterial infections caused by methicillin-resistant Staphylococcus aureus have become limited. Therefore, new and innovative approaches are needed to combat such life-threatening infections. Virulence factor expression in S. aureus is regulated in a cell density-dependent manner using "quorum sensing," which involves generation and secretion of autoinducing peptides (AIPs) into the surrounding environment to activate a bacterial sensor kinase at a particular threshold concentration. Mouse monoclonal antibody AP4-24H11 was shown previously to blunt quorum sensing-mediated changes in gene expression in vitro and protect mice from a lethal dose of S. aureus by sequestering the AIP signal. We have elucidated the crystal structure of the AP4-24H11 Fab in complex with AIP-4 at 2.5 Å resolution to determine its mechanism of ligand recognition. A key Glu(H95) provides much of the binding specificity through formation of hydrogen bonds with each of the four amide nitrogens in the AIP-4 macrocyclic ring. Importantly, these structural data give clues as to the interactions between the cognate staphylococcal AIP receptors AgrC and the AIPs, as AP4-24H11·AIP-4 binding recapitulates features that have been proposed for AgrC-AIP recognition. Additionally, these structural insights may enable the engineering of AIP cross-reactive antibodies or quorum quenching vaccines for use in active or passive immunotherapy for prevention or treatment of S. aureus infections.


  • Organizational Affiliation
    • Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 97.06 kDa 
  • Atom Count: 7,000 
  • Modeled Residue Count: 866 
  • Deposited Residue Count: 878 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AP4-24H11 Light ChainA,
D [auth L]
218Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AP4-24H11 Heavy ChainB,
C [auth H]
213Mus musculusMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Agr autoinducing peptideE [auth C],
F [auth D]
8N/AMutation(s): 0 
UniProt
Find proteins for Q9F6Z3 (Staphylococcus aureus)
Explore Q9F6Z3 
Go to UniProtKB:  Q9F6Z3
Entity Groups
UniProt GroupQ9F6Z3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A]
I [auth A]
J [auth A]
K [auth B]
L [auth H]
G [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth H],
N [auth L],
O [auth L],
P [auth L],
Q [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A],
M [auth L]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.239 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.36α = 90
b = 98.498β = 114.03
c = 73.67γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Structure summary