9G6Q | pdb_00009g6q

scFv IP11 in complex with rocuronium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.189 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Antibody-secreting cell repertoires hold high-affinity anti-rocuronium specificities that can induce anaphylaxis in vivo.

Dejoux, A.Zhu, Q.Woolfe, A.Godon, O.Ellouze, S.Mottet, G.Castrillon, C.Gillis, C.Pecalvel, C.Ganneau, C.Iannascoli, B.Lemoine, F.Saul, F.England, P.Reber, L.L.Gouel-Cheron, A.de Chaisemartin, L.Haouz, A.Millot, G.A.Bay, S.Gerard, A.Jonsson, F.Chollet-Martin, S.Bruhns, P.

(2025) J Allergy Clin Immunol 155: 1557-1574

  • DOI: https://doi.org/10.1016/j.jaci.2025.01.025
  • Primary Citation of Related Structures:  
    9G6Q, 9G6R, 9G6S

  • PubMed Abstract: 

    Neuromuscular blocking agents (NMBA) are muscle relaxants used to assist mechanical ventilation but lead in 1/10,000 anesthesia to severe acute hypersensitivity reactions i.e., anaphylaxis. Incidences vary between types of NMBAs. Rocuronium, a widely used non-depolarizing aminosteroid NMBA, induces among the highest anaphylaxis rates. Rocuronium-induced anaphylaxis is proposed to rely on pre-existing rocuronium-binding antibodies, but no such antibodies have ever been identified. Identify rocuronium-specific antibody repertoires from plasma cells or plasmablasts of rocuronium-immunized mice, and determine the affinities, structures and anaphylactogenic potential of these antibodies for rocuronium. Herein, we engrafted rocuronium onto carrier proteins allowing immunization of mice against rocuronium, screening for rocuronium-specific antibody responses, and sorting of rocuronium-specific plasma cells using droplet microfluidics coupled to single-cell antibody gene (VH and VL) sequencing. The two different repertoires of >500 VH-VL pairs were oligoclonal, comprised of three major clonal families, and displayed convergence. Expressed as human IgG1, these antibodies demonstrated subnanomolar affinities for rocuronium with families either monospecific for rocuronium or cross-reactive only for closely-related NMBAs. Expressed as human IgE, they triggered human mast cell and basophil activation, and severe passive systemic anaphylaxis in mice humanized for the IgE receptor FcεRI. Co-crystal structures between rocuronium and antibody representatives of three different VH-VL families revealed distinct interaction modes with, however, the ammonium group involved systematically in the binding interface. This work identifies the epitopes of antibody reactivity to rocuronium, demonstrates anaphylactogenic potential of anti-rocuronium IgE and establishes the first mouse model of NMBA anaphylaxis.


  • Organizational Affiliation
    • Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
scFv-IP11A [auth H]121Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
scFv-IP11B [auth L]132Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.879α = 90
b = 63.685β = 90
c = 80.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Pasteur InstituteFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references