7QXC

Recognition of Staphylococcus aureus wall teichoic acid analogue SA533 (compound 1) by Fab4461


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Antibody Recognition of Different Staphylococcus aureus Wall Teichoic Acid Glycoforms.

Di Carluccio, C.Soriano-Maldonado, P.Berni, F.de Haas, C.J.C.Temming, A.R.Hendriks, A.Ali, S.Molinaro, A.Silipo, A.van Sorge, N.M.van Raaij, M.J.Codee, J.D.C.Marchetti, R.

(2022) ACS Cent Sci 8: 1383-1392

  • DOI: https://doi.org/10.1021/acscentsci.2c00125
  • Primary Citation of Related Structures:  
    7QXC, 7QXD, 7QXE

  • PubMed Abstract: 

    Wall teichoic acids (WTAs) are glycopolymers decorating the surface of Gram-positive bacteria and potential targets for antibody-mediated treatments against Staphylococcus aureus , including methicillin-resistant (MRSA) strains. Through a combination of glycan microarray, synthetic chemistry, crystallography, NMR, and computational studies, we unraveled the molecular and structural details of fully defined synthetic WTA fragments recognized by previously described monoclonal antibodies (mAbs 4461 and 4497). Our results unveiled the structural requirements for the discriminatory recognition of α- and β-GlcNAc-modified WTA glycoforms by the complementarity-determining regions (CDRs) of the heavy and light chains of the mAbs. Both mAbs interacted not only with the sugar moiety but also with the phosphate groups as well as residues in the ribitol phosphate (RboP) units of the WTA backbone, highlighting their significant role in ligand specificity. Using elongated WTA fragments, containing two sugar modifications, we also demonstrated that the internal carbohydrate moiety of α-GlcNAc-modified WTA is preferentially accommodated in the binding pocket of mAb 4461 with respect to the terminal moiety. Our results also explained the recently documented cross-reactivity of mAb 4497 for β-1,3/β-1,4-GlcNAc-modified WTA, revealing that the flexibility of the RboP backbone is crucial to allow positioning of both glycans in the antibody binding pocket.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126Naples, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 4461 heavy chainA [auth HHH]239Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 4461 light chainB [auth LLL]220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G6N (Subject of Investigation/LOI)
Query on G6N

Download Ideal Coordinates CCD File 
E [auth LLL][(2~{S},3~{S},4~{R})-4-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2,3-bis(oxidanyl)-5-[oxidanyl-[(2~{R})-2-oxidanylpropoxy]phosphoryl]oxy-pentyl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate
C23 H47 N O24 P2
CTFVIOIQZHDZBZ-PFSLZBRHSA-N
3CX
Query on 3CX

Download Ideal Coordinates CCD File 
C [auth HHH](2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid
C9 H19 N O4 S
INEWUCPYEUEQTN-VIFPVBQESA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth HHH],
F [auth LLL],
G [auth LLL],
H [auth LLL]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.191α = 90
b = 65.448β = 112.899
c = 74.338γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainBFU2017-82207-P

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description