7O4W | pdb_00007o4w

Crystal structure of diphtheria toxin mutant CRM197 with a disulphide bond replaced by a Cys-Acetone-Cys bridge


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Retaining the structural integrity of disulfide bonds in diphtheria toxoid carrier protein is crucial for the effectiveness of glycoconjugate vaccine candidates.

Carboni, F.Kitowski, A.Sorieul, C.Veggi, D.Marques, M.C.Oldrini, D.Balducci, E.Brogioni, B.Del Bino, L.Corrado, A.Angiolini, F.Dello Iacono, L.Margarit, I.Romano, M.R.Bernardes, G.J.L.Adamo, R.

(2022) Chem Sci 13: 2440-2449

  • DOI: https://doi.org/10.1039/d1sc01928g
  • Primary Citation Related Structures: 
    7O4W

  • PubMed Abstract: 

    The introduction of glycoconjugate vaccines marks an important point in the fight against various infectious diseases. The covalent conjugation of relevant polysaccharide antigens to immunogenic carrier proteins enables the induction of a long-lasting and robust IgG antibody response, which is not observed for pure polysaccharide vaccines. Although there has been remarkable progress in the development of glycoconjugate vaccines, many crucial parameters remain poorly understood. In particular, the influence of the conjugation site and strategy on the immunogenic properties of the final glycoconjugate vaccine is the focus of intense research. Here, we present a comparison of two cysteine selective conjugation strategies, elucidating the impact of both modifications on the structural integrity of the carrier protein, as well as on the immunogenic properties of the resulting glycoconjugate vaccine candidates. Our work suggests that conjugation chemistries impairing structurally relevant elements of the protein carrier, such as disulfide bonds, can have a dramatic effect on protein immunogenicity.


  • Organizational Affiliation
    • GSK Via Fiorentina 10 53100 Siena Italy roberto.x.adamo@gsk.com.

Macromolecule Content 

  • Total Structure Weight: 59.1 kDa 
  • Atom Count: 4,113 
  • Modeled Residue Count: 520 
  • Deposited Residue Count: 535 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Diphtheria toxin535Corynebacterium diphtheriaeMutation(s): 1 
EC: 2.4.2.36
UniProt
Find proteins for Q6NK15 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NK15 
Go to UniProtKB:  Q6NK15
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NK15
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on PGE



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
4Y8
(Subject of Investigation/LOI)

Query on 4Y8



Download:Ideal Coordinates CCD File
B [auth A]1-hydroxypropan-2-one
C3 H6 O2
XLSMFKSTNGKWQX-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.996α = 90
b = 97.996β = 90
c = 98.267γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description