5F1W

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.161 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.223 

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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
B, C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  9 Unique
IDChainsTypeFormula2D DiagramParent
DHI
Query on DHI
A, B, C, D, E, F
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DSN
Query on DSN
A, B, C, D, E, F
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
A, B, C, D, E, F
D-PEPTIDE LINKINGC5 H11 N O2

--

DTH
Query on DTH
A, B, C, D, E, F
D-PEPTIDE LINKINGC4 H9 N O3

--

DLE
Query on DLE
A, B, C, D, E, F
D-PEPTIDE LINKINGC6 H13 N O2

--

DAL
Query on DAL
A, B, C, D, E, F
D-PEPTIDE LINKINGC3 H7 N O2

--

IOY
Query on IOY
A, B, C, D, E, F
D-PEPTIDE LINKINGC9 H10 I N O2

--

MV9
Query on MV9
A, B, C, D, E, F
D-peptide linkingC6 H13 N O2

--

ORD
Query on ORD
A, B, C, D, E, F
D-PEPTIDE LINKINGC5 H12 N2 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.161 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.223 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 77.910α = 90.00
b = 77.910β = 90.00
c = 77.910γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction

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