6TKD

ChiLob 7/4 H2 HC-C228S F(ab')2

• PDB DOI: https://doi.org/10.2210/pdb6TKD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-11-28 Released: 2021-06-09 
• Deposition Author(s): Orr, C.M., Fisher, H., Tews, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.173 

Literature

Hinge disulfides in human IgG2 CD40 antibodies modulate receptor signaling by regulation of conformation and flexibility.

Orr, C.M., Fisher, H., Yu, X., Chan, C.H., Gao, Y., Duriez, P.J., Booth, S.G., Elliott, I., Inzhelevskaya, T., Mockridge, I., Penfold, C.A., Wagner, A., Glennie, M.J., White, A.L., Essex, J.W., Pearson, A.R., Cragg, M.S., Tews, I.

(2022) Sci Immunol 7: eabm3723-eabm3723

• PubMed: 35857577 
• DOI: https://doi.org/10.1126/sciimmunol.abm3723
• Primary Citation of Related Structures:  
  6TKB, 6TKC, 6TKD, 6TKE, 6TKF


• PubMed Abstract: 
  

  Antibodies protect from infection, underpin successful vaccines and elicit therapeutic responses in otherwise untreatable cancers and autoimmune conditions. The human IgG2 isotype displays a unique capacity to undergo disulfide shuffling in the hinge region, leading to modulation of its ability to drive target receptor signaling (agonism) in a variety of important immune receptors, through hitherto unexplained molecular mechanisms. To address the underlying process and reveal how hinge disulfide orientation affects agonistic activity, we generated a series of cysteine to serine exchange variants in the hinge region of the clinically relevant monoclonal antibody ChiLob7/4, directed against the key immune receptor CD40. We report how agonistic activity varies with disulfide pattern and is afforded by the presence of a disulfide crossover between F(ab) arms in the agonistic forms, independently of epitope, as observed in the determined crystallographic structures. This structural "switch" affects directly on antibody conformation and flexibility. Small-angle x-ray scattering and ensemble modeling demonstrated that the least flexible variants adopt the fewest conformations and evoke the highest levels of receptor agonism. This covalent change may be amenable for broad implementation to modulate receptor signaling in an epitope-independent manner in future therapeutics.

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Organizational Affiliation: 

University of Southampton, Biological Sciences, Southampton SO17 1BJ, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS, gel filtration, mass spectrometry, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 48.56 kDa 
• Atom Count: 3,913 
• Modelled Residue Count: 434 
• Deposited Residue Count: 445 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chilob 7/4 H2 heavy chain C228S	A [auth HHH]	231	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chilob 7/4 H2 kappa chain	B [auth LLL]	214	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.173 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.021	α = 90
b = 148.021	β = 90
c = 46.139	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Orr, C.M., Fisher, H., Tews, I.

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description