8QXC | pdb_00008qxc

Crystal structure of antibody Fab MIL-3 with PenG-Lys

• PDB DOI: https://doi.org/10.2210/pdb8QXC/pdb

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


• Deposited: 2023-10-24 Released: 2024-07-31 
• Deposition Author(s): Moynie, L., Naismith, J.H.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Models: experimental

Literature

Covalent penicillin-protein conjugates elicit anti-drug antibodies that are clonally and functionally restricted.

Deimel, L.P., Moynie, L., Sun, G., Lewis, V., Turner, A., Buchanan, C.J., Burnap, S.A., Kutuzov, M., Kobras, C.M., Demyaneko, Y., Mohammed, S., Stracy, M., Struwe, W.B., Baldwin, A.J., Naismith, J., Davis, B.G., Sattentau, Q.J.

(2024) Nat Commun 15: 6851-6851

• PubMed: 39127707 
• DOI: https://doi.org/10.1038/s41467-024-51138-7
• Primary Citation Related Structures: 
  8QXC


• PubMed Abstract: 
  

  Many archetypal and emerging classes of small-molecule therapeutics form covalent protein adducts. In vivo, both the resulting conjugates and their off-target side-conjugates have the potential to elicit antibodies, with implications for allergy and drug sequestration. Although β-lactam antibiotics are a drug class long associated with these immunological phenomena, the molecular underpinnings of off-target drug-protein conjugation and consequent drug-specific immune responses remain incomplete. Here, using the classical β-lactam penicillin G (PenG), we probe the B and T cell determinants of drug-specific IgG responses to such conjugates in mice. Deep B cell clonotyping reveals a dominant murine clonal antibody class encompassing phylogenetically-related IGHV1, IGHV5 and IGHV10 subgroup gene segments. Protein NMR and x-ray structural analyses reveal that these drive structurally convergent binding modes in adduct-specific antibody clones. Their common primary recognition mechanisms of the penicillin side-chain moiety (phenylacetamide in PenG)-regardless of CDRH3 length-limits cross-reactivity against other β-lactam antibiotics. This immunogenetics-guided discovery of the limited binding solutions available to antibodies against side products of an archetypal covalent inhibitor now suggests future potential strategies for the 'germline-guided reverse engineering' of such drugs away from unwanted immune responses.

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Organizational Affiliation: 
• Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK. [e-mail].
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA. [e-mail].
Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford, OX11 0FA, UK.
Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.
Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, OX1 3QU, UK.
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
Department of Pharmacology, University of Oxford, Oxford, OX1 3QT, UK.
Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford, OX11 0FA, UK. [e-mail].
Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK. [e-mail].
Department of Pharmacology, University of Oxford, Oxford, OX1 3QT, UK. [e-mail].
Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK. [e-mail].
The Max Delbrück Centre for Molecular Medicine, Campus Berlin-Buch, 13125, Berlin, Germany. [e-mail].
Experimental and Clinical Research Center (ECRC), Charité Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany. [e-mail].

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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 164.16 kDa 
• Atom Count: 9,890 
• Modeled Residue Count: 1,271 
• Deposited Residue Count: 1,491 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of FAB MIL-3	A [auth H], B [auth A], E [auth C]	264	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of FAB MIL-3	C [auth L], D [auth B], F [auth D]	233	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X5X (Subject of Investigation/LOI)	G [auth H], H [auth A]	(2R,4S)-2-[(1R)-2-[[(5S)-5-acetamido-6-oxidanyl-6-oxidanylidene-hexyl]amino]-2-oxidanylidene-1-(2-phenylethanoylamino)ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C24 H34 N4 O7 S JXFMICAVKFQPRG-GZMOKQHVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.566	α = 90
b = 113.236	β = 108.8
c = 82.873	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Moynie, L., Naismith, J.H.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release
  
• Version 1.1: 2024-08-21
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary