Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 43.63 kDa 
• Atom Count: 3405 
• Residue Count: 386 
• Unique protein chains: 1

3Q28

Cyrstal structure of human alpha-synuclein (58-79) fused to maltose binding protein (MBP)

• DOI: 10.2210/pdb3Q28/pdb

• Classification: SUGAR BINDING PROTEIN, PROTEIN FIBRIL
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-19 Released: 2011-06-01 
• Deposition Author(s): Zhao, M., Sawaya, M.R., Cascio, D., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.173 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

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

• PubMed: 21462277 
• DOI: 10.1002/pro.630
• Primary Citation of Related Structures:  
  3Q25, 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein/alpha-synuclein chimeric protein	A	393	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: SNCA
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P37840 (Homo sapiens) Explore P37840  Go to UniProtKB:  P37840
NIH Common Fund Data Resources
PHAROS:  P37840 GTEx:  ENSG00000145335

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide /  Nutrient		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.173 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.54	α = 90
b = 48.57	β = 94.23
c = 57.85	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-19 
• Released Date: 2011-06-01 
Deposition Author(s): Zhao, M., Sawaya, M.R., Cascio, D., Eisenberg, D.

Revision History 

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-10-11
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary