7QXC | pdb_00007qxc

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

• PDB DOI: https://doi.org/10.2210/pdb7QXC/pdb

• Classification: CARBOHYDRATE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-01-26 Released: 2022-08-31 
• Deposition Author(s): Soriano-Maldonado, P., van Raaij, M.J.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.174 (DCC) 

Starting Model: experimental

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

• PubMed: 36313161 
• DOI: https://doi.org/10.1021/acscentsci.2c00125
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126Naples, Italy.
Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Calle Darwin 3, 28049Madrid, Spain.
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands.
Medical Microbiology, UMC Utrecht, Utrecht University, 3508Utrecht, The Netherlands.
Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZAmsterdam, The Netherlands.
Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC, 1105 AZAmsterdam, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.05 kDa 
• Atom Count: 3,835 
• Modeled Residue Count: 435 
• Deposited Residue Count: 459 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 4461 heavy chain	A [auth HHH]	239	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 4461 light chain	B [auth LLL]	220	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G6N (Subject of Investigation/LOI)	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	C [auth HHH]	(2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid C9 H19 N O4 S INEWUCPYEUEQTN-VIFPVBQESA-N
PEG	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 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.174 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.191	α = 90
b = 65.448	β = 112.899
c = 74.338	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Soriano-Maldonado, P., van Raaij, M.J.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	BFU2017-82207-P

Revision History  

• 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
• Version 1.3: 2024-10-23
  Changes: Structure summary