Structure of a single domain camelid antibody fragment in complex with a C-terminal peptide of alpha-synuclein

Experimental Data Snapshot

  • Resolution: 1.62 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 

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Structure and Properties of a Complex of Alpha-Synuclein and a Single-Domain Camelid Antibody.

De Genst, E.J.Guilliams, T.Wellens, J.O'Day, E.M.Waudby, C.A.Meehan, S.Dumoulin, M.Hsu, S.-T.D.Cremades, N.Verschueren, K.H.G.Pardon, E.Wyns, L.Steyaert, J.Christodoulou, J.Dobson, C.M.

(2010) J Mol Biol 402: 326

  • DOI: https://doi.org/10.1016/j.jmb.2010.07.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The aggregation of the intrinsically disordered protein α-synuclein to form fibrillar amyloid structures is intimately associated with a variety of neurological disorders, most notably Parkinson's disease. The molecular mechanism of α-synuclein aggregation and toxicity is not yet understood in any detail, not least because of the paucity of structural probes through which to study the behavior of such a disordered system. Here, we describe an investigation involving a single-domain camelid antibody, NbSyn2, selected by phage display techniques to bind to α-synuclein, including the exploration of its effects on the in vitro aggregation of the protein under a variety of conditions. We show using isothermal calorimetric methods that NbSyn2 binds specifically to monomeric α-synuclein with nanomolar affinity and by means of NMR spectroscopy that it interacts with the four C-terminal residues of the protein. This latter finding is confirmed by the determination of a crystal structure of NbSyn2 bound to a peptide encompassing the nine C-terminal residues of α-synuclein. The NbSyn2:α-synuclein interaction is mediated mainly by side-chain interactions while water molecules cross-link the main-chain atoms of α-synuclein to atoms of NbSyn2, a feature we believe could be important in intrinsically disordered protein interactions more generally. The aggregation behavior of α-synuclein at physiological pH, including the morphology of the resulting fibrillar structures, is remarkably unaffected by the presence of NbSyn2 and indeed we show that NbSyn2 binds strongly to the aggregated as well as to the soluble forms of α-synuclein. These results give strong support to the conjecture that the C-terminal region of the protein is not directly involved in the mechanism of aggregation and suggest that binding of NbSyn2 could be a useful probe for the identification of α-synuclein aggregation in vitro and possibly in vivo.

  • Organizational Affiliation

    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEAVY CHAIN VARIABLE DOMAIN FROM DROMEDARY126Camelus dromedariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-SYNUCLEIN PEPTIDE9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P37840 (Homo sapiens)
Explore P37840 
Go to UniProtKB:  P37840
PHAROS:  P37840
GTEx:  ENSG00000145335 
Entity Groups  
UniProt GroupP37840
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.62 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.17α = 90
b = 63.12β = 90
c = 62.87γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-08-24
    Changes: Database references, Structure summary, Version format compliance
  • Version 1.2: 2017-03-29
    Changes: Other
  • Version 1.3: 2019-07-24
    Changes: Data collection
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description