6DWI | pdb_00006dwi

Structure of the 4462 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.249 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6DWI

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structural investigation of human S. aureus-targeting antibodies that bind wall teichoic acid.

Fong, R.Kajihara, K.Chen, M.Hotzel, I.Mariathasan, S.Hazenbos, W.L.W.Lupardus, P.J.

(2018) MAbs 10: 979-991

  • DOI: https://doi.org/10.1080/19420862.2018.1501252
  • Primary Citation Related Structures: 
    6DW2, 6DWA, 6DWC, 6DWI

  • PubMed Abstract: 

    Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a growing health threat worldwide. Efforts to identify novel antibodies that target S. aureus cell surface antigens are a promising direction in the development of antibiotics that can halt MRSA infection. We biochemically and structurally characterized three patient-derived MRSA-targeting antibodies that bind to wall teichoic acid (WTA), which is a polyanionic surface glycopolymer. In S. aureus, WTA exists in both α- and β-forms, based on the stereochemistry of attachment of a N-acetylglucosamine residue to the repeating phosphoribitol sugar unit. We identified a panel of antibodies cloned from human patients that specifically recognize the α or β form of WTA, and can bind with high affinity to pathogenic wild-type strains of S. aureus bacteria. To investigate how the β-WTA specific antibodies interact with their target epitope, we determined the X-ray crystal structures of the three β-WTA specific antibodies, 4462, 4497, and 6078 (Protein Data Bank IDs 6DWI, 6DWA, and 6DW2, respectively), bound to a synthetic WTA epitope. These structures reveal that all three of these antibodies, while utilizing distinct antibody complementarity-determining region sequences and conformations to interact with β-WTA, fulfill two recognition principles: binding to the β-GlcNAc pyranose core and triangulation of WTA phosphate residues with polar contacts. These studies reveal the molecular basis for targeting a unique S. aureus cell surface epitope and highlight the power of human patient-based antibody discovery techniques for finding novel pathogen-targeting therapeutics.


  • Organizational Affiliation
    • a Department of Structural Biology , Genentech , South San Francisco , CA , USA.

Macromolecule Content 

  • Total Structure Weight: 411.76 kDa 
  • Atom Count: 26,175 
  • Modeled Residue Count: 3,337 
  • Deposited Residue Count: 3,808 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4462 Fab Light Chain
A, C, E, G, I
A, C, E, G, I, K, M, O
233Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
4462 Fab Heavy chain
B, D, F, H, J
B, D, F, H, J, L, N, P
243Homo sapiensMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HD4

Query on HD4



Download:Ideal Coordinates CCD File
BA [auth L],
T [auth D],
X [auth H],
Z [auth J]
4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol
C13 H26 N O13 P
UTDJSTSCOBYMHN-SKCKNYEVSA-N
FLC

Query on FLC



Download:Ideal Coordinates CCD File
W [auth G]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth J],
Y [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth O]
Q [auth A]
R [auth B]
S [auth C]
U [auth F]
CA [auth O],
Q [auth A],
R [auth B],
S [auth C],
U [auth F],
V [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.249 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.573α = 90
b = 114.097β = 90.46
c = 128.301γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary