5F1T

Crystal structure of a macrocyclic peptide containing fragments from alpha-synuclein 36-55.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.971 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray Crystallographic Structure of Oligomers Formed by a Toxic beta-Hairpin Derived from alpha-Synuclein: Trimers and Higher-Order Oligomers.

Salveson, P.J.Spencer, R.K.Nowick, J.S.

(2016) J.Am.Chem.Soc. 138: 4458-4467

  • DOI: 10.1021/jacs.5b13261
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Oligomeric assemblies of the protein α-synuclein are thought to cause neurodegeneration in Parkinson's disease and related synucleinopathies. Characterization of α-synuclein oligomers at high resolution is an outstanding challenge in the field of str ...

    Oligomeric assemblies of the protein α-synuclein are thought to cause neurodegeneration in Parkinson's disease and related synucleinopathies. Characterization of α-synuclein oligomers at high resolution is an outstanding challenge in the field of structural biology. The absence of high-resolution structures of oligomers formed by α-synuclein impedes understanding the synucleinopathies at the molecular level. This paper reports the X-ray crystallographic structure of oligomers formed by a peptide derived from residues 36-55 of α-synuclein. The peptide 1a adopts a β-hairpin structure, which assembles in a hierarchical fashion. Three β-hairpins assemble to form a triangular trimer. Three copies of the triangular trimer assemble to form a basket-shaped nonamer. Two nonamers pack to form an octadecamer. Molecular modeling suggests that full-length α-synuclein may also be able to assemble in this fashion. Circular dichroism spectroscopy demonstrates that peptide 1a interacts with anionic lipid bilayer membranes, like oligomers of full-length α-synuclein. LDH and MTT assays demonstrate that peptide 1a is toxic toward SH-SY5Y cells. Comparison of peptide 1a to homologues suggests that this toxicity results from nonspecific interactions with the cell membrane. The oligomers formed by peptide 1a are fundamentally different than the proposed models of the fibrils formed by α-synuclein and suggest that α-Syn36-55, rather than the NAC, may nucleate oligomer formation.


    Organizational Affiliation

    Department of Chemistry, University of California Irvine , Irvine, California 92697-2025, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrocyclic peptide
A, B, C, D, E, F
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
C
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ORN
Query on ORN
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H10 I N O2PHE
MVA
Query on MVA
A, B, C, D, E, F
L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.971 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 77.518α = 90.00
b = 77.518β = 90.00
c = 77.518γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references