Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.51 kDa 
• Atom Count: 1235 
• Residue Count: 132 
• Unique protein chains: 2

2X6M

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

• DOI: 10.2210/pdb2X6M/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Camelus dromedarius, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-18 Released: 2010-06-23 
• Deposition Author(s): DeGenst, E., 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.203 
• R-Value Work: 0.156 
• R-Value Observed: 0.160 

Literature

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

• PubMed: 20620148 
• DOI: 10.1016/j.jmb.2010.07.001
• Primary Citation of Related Structures:  
  2X6M


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAVY CHAIN VARIABLE DOMAIN FROM DROMEDARY	A	126	Camelus dromedarius	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-SYNUCLEIN PEPTIDE	B	9	Homo sapiens	Mutation(s): 0  Gene Names: SNCA, NACP, PARK1
Find proteins for P37840 (Homo sapiens) Explore P37840  Go to UniProtKB:  P37840
NIH Common Fund Data Resources
PHAROS:  P37840 GTEx:  ENSG00000145335

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 60.17	α = 90
b = 63.12	β = 90
c = 62.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-18 
• Released Date: 2010-06-23 
Deposition Author(s): DeGenst, E., 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.

Revision History 

• 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