9G6S | pdb_00009g6s

Fab-IP2 in complex with rocuronium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.253 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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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 Related Structures: 
    9G6Q, 9G6R, 9G6S

  • PubMed Abstract: 

    Neuromuscular blocking agents (NMBAs) are muscle relaxants used to assist mechanical ventilation but lead in 1 per 10,000 anesthesia cases to severe acute hypersensitivity reactions-that is, anaphylaxis. Incidences vary between types of NMBAs. Rocuronium, a widely used nondepolarizing aminosteroid NMBA, induces among the highest anaphylaxis rates. Rocuronium-induced anaphylaxis is proposed to rely on preexisting rocuronium-binding antibodies, but no such antibodies have ever been identified. We sought to identify rocuronium-specific antibody repertoires from plasma cells or plasmablasts of rocuronium-immunized mice to determine the affinities, structures, and anaphylactogenic potential of these antibodies for rocuronium. 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 microfluids coupled to single-cell antibody gene (variable heavy chain [VH] and variable light chain [VL]) sequencing. The 2 different repertoires of >500 VH-VL pairs were oligoclonal, comprised 3 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. Cocrystal structures between rocuronium and antibody representatives of 3 different VH-VL families revealed distinct interaction modes, with 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, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1222, Antibodies in Therapy and Pathology, Paris, France; Collège Doctoral, Sorbonne Université, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 47.04 kDa 
  • Atom Count: 3,338 
  • Modeled Residue Count: 421 
  • Deposited Residue Count: 432 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab-IP2 H chainA [auth H]218Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab-IP2 L chainB [auth L]214Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RBR
(Subject of Investigation/LOI)

Query on RBR



Download:Ideal Coordinates CCD File
C [auth H]rocuronium
C32 H53 N2 O4
YXRDKMPIGHSVRX-OOJCLDBCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.253 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.638α = 90
b = 131.638β = 90
c = 95.24γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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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