3Q25

Crystal structure of human alpha-synuclein (1-19) fused to maltose binding protein (MBP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of segments of alpha-synuclein fused to maltose-binding protein suggest intermediate states during amyloid formation

Zhao, M.Cascio, D.Sawaya, M.R.Eisenberg, D.

(2011) Protein Sci. 20: 996-1004

  • DOI: 10.1002/pro.630
  • Primary Citation of Related Structures:  3Q26, 3Q27, 3Q28, 3Q29

  • PubMed Abstract: 
  • Aggregates of the protein α-synuclein are the main component of Lewy bodies, the hallmark of Parkinson's disease. α-Synuclein aggregates are also found in many human neurodegenerative diseases known as synucleinopathies. In vivo, α-synuclein associat ...

    Aggregates of the protein α-synuclein are the main component of Lewy bodies, the hallmark of Parkinson's disease. α-Synuclein aggregates are also found in many human neurodegenerative diseases known as synucleinopathies. In vivo, α-synuclein associates with membranes and adopts α-helical conformations. The details of how α-synuclein converts from the functional native state to amyloid aggregates remain unknown. In this study, we use maltose-binding protein (MBP) as a carrier to crystallize segments of α-synuclein. From crystal structures of fusions between MBP and four segments of α-synuclein, we have been able to trace a virtual model of the first 72 residues of α-synuclein. Instead of a mostly α-helical conformation observed in the lipid environment, our crystal structures show α-helices only at residues 1-13 and 20-34. The remaining segments are extended loops or coils. All of the predicted fiber-forming segments based on the 3D profile method are in extended conformations. We further show that the MBP fusion proteins with fiber-forming segments from α-synuclein can also form fiber-like nano-crystals or amyloid-like fibrils. Our structures suggest intermediate states during amyloid formation of α-synuclein.


    Organizational Affiliation

    Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein/alpha-synuclein chimeric protein
A
390Homo sapiensEscherichia coli (strain K12)
This entity is chimeric
Gene Names: SNCA (NACP, PARK1), malE
Find proteins for P37840 (Homo sapiens)
Go to Gene View: SNCA
Go to UniProtKB:  P37840
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

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Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.470α = 90.00
b = 77.470β = 90.00
c = 172.640γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-02
    Type: Refinement description, Source and taxonomy