7QXD

Recognition of Staphylococcus aureus wall teichoic acid analogue SA475 (compound 2) by Fab4497


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.175 

wwPDB Validation   3D Report Full Report


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
Antibody Fab 4497 heavy chainA [auth HHH],
C [auth KKK]
236Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab 4497 light chainB [auth LLL],
D [auth MMM]
220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G5F (Subject of Investigation/LOI)
Query on G5F

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

Download Ideal Coordinates CCD File 
H [auth KKK]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth LLL],
K [auth MMM]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth LLL],
I [auth KKK]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.392α = 90
b = 113.371β = 90
c = 154.557γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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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