6FG1

CRYSTAL STRUCTURE OF FAB OF NATALIZUMAB IN COMPLEX WITH FAB OF NAA32.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A single T cell epitope drives the neutralizing anti-drug antibody response to natalizumab in multiple sclerosis patients.

Cassotta, A.Mikol, V.Bertrand, T.Pouzieux, S.Le Parc, J.Ferrari, P.Dumas, J.Auer, M.Deisenhammer, F.Gastaldi, M.Franciotta, D.Silacci-Fregni, C.Fernandez Rodriguez, B.Giacchetto-Sasselli, I.Foglierini, M.Jarrossay, D.Geiger, R.Sallusto, F.Lanzavecchia, A.Piccoli, L.

(2019) Nat Med 25: 1402-1407

  • DOI: 10.1038/s41591-019-0568-2
  • Primary Citation of Related Structures:  
    6FG2, 6FG1

  • PubMed Abstract: 
  • Natalizumab (NZM), a humanized monoclonal IgG4 antibody to α4 integrins, is used to treat patients with relapsing-remitting multiple sclerosis (MS) 1,2 , but in about 6% of the cases persistent neutralizing anti-drug antibodies (ADAs) are induced leading to therapy discontinuation 3,4 ...

    Natalizumab (NZM), a humanized monoclonal IgG4 antibody to α4 integrins, is used to treat patients with relapsing-remitting multiple sclerosis (MS) 1,2 , but in about 6% of the cases persistent neutralizing anti-drug antibodies (ADAs) are induced leading to therapy discontinuation 3,4 . To understand the basis of the ADA response and the mechanism of ADA-mediated neutralization, we performed an in-depth analysis of the B and T cell responses in two patients. By characterizing a large panel of NZM-specific monoclonal antibodies, we found that, in both patients, the response was polyclonal and targeted different epitopes of the NZM idiotype. The neutralizing activity was acquired through somatic mutations and correlated with a slow dissociation rate, a finding that was supported by structural data. Interestingly, in both patients, the analysis of the CD4 + T cell response, combined with mass spectrometry-based peptidomics, revealed a single immunodominant T cell epitope spanning the FR2-CDR2 region of the NZM light chain. Moreover, a CDR2-modified version of NZM was not recognized by T cells, while retaining binding to α4 integrins. Collectively, our integrated analysis identifies the basis of T-B collaboration that leads to ADA-mediated therapeutic resistance and delineates an approach to design novel deimmunized antibodies for autoimmune disease and cancer treatment.


    Organizational Affiliation

    Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland. luca.piccoli@irb.usi.ch.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN OF FAB NAA32A241Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT CHAIN OF FAB NAA32B [auth D]215Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN OF FAB NATALIZUMABC [auth H]234Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT CHAIN OF FAB NATALIZUMABD [auth L]213Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth H], F [auth H], G [auth L]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.101α = 90
b = 189.101β = 90
c = 87.259γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references