6H1F

Structure of the nanobody-stabilized gelsolin D187N variant (second domain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variant.

Giorgino, T.Mattioni, D.Hassan, A.Milani, M.Mastrangelo, E.Barbiroli, A.Verhelle, A.Gettemans, J.Barzago, M.M.Diomede, L.de Rosa, M.

(2019) Biochim Biophys Acta Mol Basis Dis 1865: 648-660

  • DOI: 10.1016/j.bbadis.2019.01.010

  • PubMed Abstract: 
  • AGel amyloidosis, formerly known as familial amyloidosis of the Finnish-type, is caused by pathological aggregation of proteolytic fragments of plasma gelsolin. So far, four mutations in the gelsolin gene have been reported as responsible for the dis ...

    AGel amyloidosis, formerly known as familial amyloidosis of the Finnish-type, is caused by pathological aggregation of proteolytic fragments of plasma gelsolin. So far, four mutations in the gelsolin gene have been reported as responsible for the disease. Although D187N is the first identified variant and the best characterized, its structure has been hitherto elusive. Exploiting a recently-developed nanobody targeting gelsolin, we were able to stabilize the G2 domain of the D187N protein and obtained, for the first time, its high-resolution crystal structure. In the nanobody-stabilized conformation, the main effect of the D187N substitution is the impairment of the calcium binding capability, leading to a destabilization of the C-terminal tail of G2. However, molecular dynamics simulations show that in the absence of the nanobody, D187N-mutated G2 further misfolds, ultimately exposing its hydrophobic core and the furin cleavage site. The nanobody's protective effect is based on the enhancement of the thermodynamic stability of different G2 mutants (D187N, G167R and N184K). In particular, the nanobody reduces the flexibility of dynamic stretches, and most notably decreases the conformational entropy of the C-terminal tail, otherwise stabilized by the presence of the Ca 2+ ion. A Caenorhabditis elegans-based assay was also applied to quantify the proteotoxic potential of the mutants and determine whether nanobody stabilization translates into a biologically relevant effect. Successful protection from G2 toxicity in vivo points to the use of C. elegans as a tool for investigating the mechanisms underlying AGel amyloidosis and rapidly screen new therapeutics.


    Organizational Affiliation

    Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.,Nanobody Lab, Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.,Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy.,Department of Molecular Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy; Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy; Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy. Electronic address: matteo.derosa@cnr.it.,Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, Milano, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy; Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
gelsolin nanobody, Nb11
A
140N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gelsolin
B
119Homo sapiensMutation(s): 1 
Gene Names: GSN
Find proteins for P06396 (Homo sapiens)
Go to Gene View: GSN
Go to UniProtKB:  P06396
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.859α = 90.00
b = 46.835β = 90.00
c = 132.111γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Amyloidosis FoundationUnited States--

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release