BMRB Entry 25518

Name: Atomic-resolution structure of alpha-synuclein fibrils
Published: 2016-03-15

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PDB ID: 2n0a
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25518
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Atomic-resolution structure of alpha-synuclein fibrils

Deposition date:

2015-03-04

Original release date:

2016-03-15

Authors:

Tuttle, Marcus; Comellas, Gemma; Nieuwkoop, Andrew; Covell, Dustin; Berthold, Deborah; Kloepper, Kathryn; Courtney, Joseph; Kim, Jae; Schwieters, Charles; Lee, Virginia; George, Julia; Rienstra, Chad

Citation:

Citation: Tuttle, Marcus; Comellas, Gemma; Nieuwkoop, Andrew; Covell, Dustin; Berthold, Deborah; Kloepper, Kathryn; Courtney, Joseph; Kim, Jae; Barclay, Alexander; Kendall, Amy; Wan, William; Stubbs, Gerald; Schwieters, Charles; Lee, Virginia; George, Julia; Rienstra, Chad. "Solid-state NMR structure of a pathogenic fibril of full-length human {alpha}-Synuclein" Nature Struc. Mol. Biol. 23, 409-415 (2016).
PubMed: 27018801

Assembly members:

Assembly members:
alpha-synuclein, polymer, 140 residues, 14476.245 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a-AS

Entity Sequences (FASTA):

Entity Sequences (FASTA):
alpha-synuclein: MDVFMKGLSKAKEGVVAAAE KTKQGVAEAAGKTKEGVLYV GSKTKEGVVHGVATVAEKTK EQVTNVGGAVVTGVTAVAQK TVEGAGSIAAATGFVKKDQL GKNEEGAPQEGILEDMPVDP DNEAYEMPSEEGYQDYEPEA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	135
15N chemical shifts	39

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	strand_1	1
2	strand_2	1
3	strand_3	1
4	strand_4	1
5	strand_5	1
6	strand_6	1
7	strand_7	1
8	strand_8	1
9	strand_9	1
10	strand_10	1

Entities:

Entity 1, strand_1 140 residues - 14476.245 Da.

1	MET	ASP	VAL	PHE	MET	LYS	GLY	LEU	SER	LYS
2	ALA	LYS	GLU	GLY	VAL	VAL	ALA	ALA	ALA	GLU
3	LYS	THR	LYS	GLN	GLY	VAL	ALA	GLU	ALA	ALA
4	GLY	LYS	THR	LYS	GLU	GLY	VAL	LEU	TYR	VAL
5	GLY	SER	LYS	THR	LYS	GLU	GLY	VAL	VAL	HIS
6	GLY	VAL	ALA	THR	VAL	ALA	GLU	LYS	THR	LYS
7	GLU	GLN	VAL	THR	ASN	VAL	GLY	GLY	ALA	VAL
8	VAL	THR	GLY	VAL	THR	ALA	VAL	ALA	GLN	LYS
9	THR	VAL	GLU	GLY	ALA	GLY	SER	ILE	ALA	ALA
10	ALA	THR	GLY	PHE	VAL	LYS	LYS	ASP	GLN	LEU
11	GLY	LYS	ASN	GLU	GLU	GLY	ALA	PRO	GLN	GLU
12	GLY	ILE	LEU	GLU	ASP	MET	PRO	VAL	ASP	PRO
13	ASP	ASN	GLU	ALA	TYR	GLU	MET	PRO	SER	GLU
14	GLU	GLY	TYR	GLN	ASP	TYR	GLU	PRO	GLU	ALA

Samples:

sample_1: alpha-synuclein, [U-100% 13C; U-100% 15N], 66 % w/w; H2O 34 % w/w

sample_2: alpha-synuclein, [U-100% 13C 1,3-Glycerol; U-100% 15N], 66 % w/w; H2O 34 % w/w

sample_3: alpha-synuclein, [U-100% 13C 2-Glycerol; U-100% 15N], 66 % w/w; H2O 34 % w/w

sample_4: alpha-synuclein, [U-25% 13C; U-25% 15N], 66 % w/w; H2O 34 % w/w

sample_5: alpha-synuclein, [U-25% 13C 1,3-Glycerol; natural abundance N][natural abundance C13, U-50% N15], 66 % w/w; H2O 34 % w/w

sample_6: alpha-synuclein, [U-25% 13C 2-Glycerol; natural abundance N][natural abundance C13, U-50% N15], 66 % w/w; H2O 34 % w/w

Adamantane: Adamantane 90 % w/w; KBr 10 % w/w

sample_conditions_1: pH: 7; pressure: 1 atm; temperature controller setting: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
Cross Polarization C1D	Adamantane	solid	sample_conditions_1
3D NCACX	sample_1	solid	sample_conditions_1
3D NCOCX	sample_1	solid	sample_conditions_1
3D CANCO	sample_1	solid	sample_conditions_1
2D CC DARR	sample_1	solid	sample_conditions_1
2D CC DARR	sample_2	solid	sample_conditions_1
3D NCOCX	sample_2	solid	sample_conditions_1
2D NC TEDOR	sample_2	solid	sample_conditions_1
2D CC DARR	sample_2	solid	sample_conditions_1
2D CC DARR	sample_2	solid	sample_conditions_1
3D NCOCX	sample_2	solid	sample_conditions_1
2D CC DARR	sample_3	solid	sample_conditions_1
3D NCACX	sample_3	solid	sample_conditions_1
2D CC DARR	sample_3	solid	sample_conditions_1
2D NC TEDOR	sample_3	solid	sample_conditions_1
2D CC DARR	sample_3	solid	sample_conditions_1
3D NCACX	sample_3	solid	sample_conditions_1
2D NC TEDOR	sample_4	solid	sample_conditions_1
2D NC TEDOR	sample_5	solid	sample_conditions_1
2D CC DARR	sample_6	solid	sample_conditions_1
2D ChhC	sample_6	solid	sample_conditions_1

Software:

X-PLOR_NIH v2.33.4, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution

SPARKY v3, T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco - data visualization, manual analysis

NMR spectrometers:

Agilent VNMRS 750 MHz
Agilent InfinityPlus 600 MHz
Agilent VNMRS 500 MHz

1	MET	ASP	VAL	PHE	MET	LYS	GLY	LEU	SER	LYS
2	ALA	LYS	GLU	GLY	VAL	VAL	ALA	ALA	ALA	GLU
3	LYS	THR	LYS	GLN	GLY	VAL	ALA	GLU	ALA	ALA
4	GLY	LYS	THR	LYS	GLU	GLY	VAL	LEU	TYR	VAL
5	GLY	SER	LYS	THR	LYS	GLU	GLY	VAL	VAL	HIS
6	GLY	VAL	ALA	THR	VAL	ALA	GLU	LYS	THR	LYS
7	GLU	GLN	VAL	THR	ASN	VAL	GLY	GLY	ALA	VAL
8	VAL	THR	GLY	VAL	THR	ALA	VAL	ALA	GLN	LYS
9	THR	VAL	GLU	GLY	ALA	GLY	SER	ILE	ALA	ALA
10	ALA	THR	GLY	PHE	VAL	LYS	LYS	ASP	GLN	LEU
11	GLY	LYS	ASN	GLU	GLU	GLY	ALA	PRO	GLN	GLU
12	GLY	ILE	LEU	GLU	ASP	MET	PRO	VAL	ASP	PRO
13	ASP	ASN	GLU	ALA	TYR	GLU	MET	PRO	SER	GLU
14	GLU	GLY	TYR	GLN	ASP	TYR	GLU	PRO	GLU	ALA

1	MET	ASP	VAL	PHE	MET	LYS	GLY	LEU	SER	LYS
2	ALA	LYS	GLU	GLY	VAL	VAL	ALA	ALA	ALA	GLU
3	LYS	THR	LYS	GLN	GLY	VAL	ALA	GLU	ALA	ALA
4	GLY	LYS	THR	LYS	GLU	GLY	VAL	LEU	TYR	VAL
5	GLY	SER	LYS	THR	LYS	GLU	GLY	VAL	VAL	HIS
6	GLY	VAL	ALA	THR	VAL	ALA	GLU	LYS	THR	LYS
7	GLU	GLN	VAL	THR	ASN	VAL	GLY	GLY	ALA	VAL
8	VAL	THR	GLY	VAL	THR	ALA	VAL	ALA	GLN	LYS
9	THR	VAL	GLU	GLY	ALA	GLY	SER	ILE	ALA	ALA
10	ALA	THR	GLY	PHE	VAL	LYS	LYS	ASP	GLN	LEU
11	GLY	LYS	ASN	GLU	GLU	GLY	ALA	PRO	GLN	GLU
12	GLY	ILE	LEU	GLU	ASP	MET	PRO	VAL	ASP	PRO
13	ASP	ASN	GLU	ALA	TYR	GLU	MET	PRO	SER	GLU
14	GLU	GLY	TYR	GLN	ASP	TYR	GLU	PRO	GLU	ALA

1	MET	ASP	VAL	PHE	MET	LYS	GLY	LEU	SER	LYS
2	ALA	LYS	GLU	GLY	VAL	VAL	ALA	ALA	ALA	GLU
3	LYS	THR	LYS	GLN	GLY	VAL	ALA	GLU	ALA	ALA
4	GLY	LYS	THR	LYS	GLU	GLY	VAL	LEU	TYR	VAL
5	GLY	SER	LYS	THR	LYS	GLU	GLY	VAL	VAL	HIS
6	GLY	VAL	ALA	THR	VAL	ALA	GLU	LYS	THR	LYS
7	GLU	GLN	VAL	THR	ASN	VAL	GLY	GLY	ALA	VAL
8	VAL	THR	GLY	VAL	THR	ALA	VAL	ALA	GLN	LYS
9	THR	VAL	GLU	GLY	ALA	GLY	SER	ILE	ALA	ALA
10	ALA	THR	GLY	PHE	VAL	LYS	LYS	ASP	GLN	LEU
11	GLY	LYS	ASN	GLU	GLU	GLY	ALA	PRO	GLN	GLU
12	GLY	ILE	LEU	GLU	ASP	MET	PRO	VAL	ASP	PRO
13	ASP	ASN	GLU	ALA	TYR	GLU	MET	PRO	SER	GLU
14	GLU	GLY	TYR	GLN	ASP	TYR	GLU	PRO	GLU	ALA