8P88 | pdb_00008p88

X-ray structure of cardiotoxic light chain H3 in complex to neutralizing nanobody C4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.233 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8P88

This is version 1.2 of the entry. See complete history

Literature

Nanobodies counteract the toxicity of an amyloidogenic light chain by stabilizing a partially open dimeric conformation.

Broggini, L.Barzago, M.M.Speranzini, V.Schulte, T.Sonzini, F.Giono, M.Romeo, M.Milani, P.Caminito, S.Mazzini, G.Rognoni, P.Merlini, G.Pappone, C.Anastasia, L.Nuvolone, M.Palladini, G.Diomede, L.Ricagno, S.

(2023) J Mol Biology 435: 168320-168320

  • DOI: https://doi.org/10.1016/j.jmb.2023.168320
  • Primary Citation Related Structures: 
    8P88, 8P89

  • PubMed Abstract: 

    Light chain amyloidosis (AL) is a systemic disease where fibrillar deposition of misfolded immunoglobulin light chains (LCs) severely affects organ function and results in poor prognosis for patients, especially when heart involvement is severe. Particularly relevant in this context is the cardiotoxicity exerted by still uncharacterized soluble LC species. Here, with the final goal of identifying alternative therapeutic strategies to tackle AL amyloidosis, we produced five llama-derived nanobodies (Nbs) specific against H3, a well-characterized amyloidogenic and cardiotoxic LC from an AL patient with severe cardiac involvement. We found that Nbs are specific and potent agents capable of abolishing H3 soluble toxicity in C. elegans in vivo model. Structural characterization of H3-Nb complexes revealed that the protective effect of Nbs is related to their ability to bind to the H3 V L domain and stabilise an unexpected partially open LC dimer in which the two V L domains no longer interact with each other. Thus, while identifying potent inhibitors of LC soluble toxicity, we also describe the first non-native structure of an amyloidogenic LC that may represent a crucial step in toxicity and aggregation mechanisms.


  • Organizational Affiliation
    • Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy.

Macromolecule Content 

  • Total Structure Weight: 35.79 kDa 
  • Atom Count: 2,734 
  • Modeled Residue Count: 333 
  • Deposited Residue Count: 337 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light Chain H3216Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody C4B [auth C]121Lama glamaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.233 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.593α = 90
b = 121.953β = 90
c = 88.675γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
STARANISOdata scaling
Cootmodel building
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Structure summary