BMRB Entry 16939

Name: WT alpha-synuclein fibrils
Published: 2011-07-07

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR16939

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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:

WT alpha-synuclein fibrils

Deposition date:

2010-05-19

Original release date:

2011-07-07

Authors:

Comellas, Gemma; Kloepper, Kathryn; Nieuwkoop, Andrew; Lemkau, Luisel; Ladror, Daniel; Ebisu, Reika; Woods, Wendy; Lipton, Andrew; George, Julia; Rienstra, Chad

Citation:

Citation: Comellas, Gemma; Lemkau, Luisel; Nieuwkoop, Andrew; Kloepper, Kathryn; Ladror, Daniel; Ebisu, Reika; Woods, Wendy; Lipton, Andrew; George, Julia; Rienstra, Chad. "Structured Regions of alpha-Synuclein Fibrils Include the Early-Onset Parkinson's Disease Mutation Sites." J. Mol. Biol. 411, 881-895 (2011).
PubMed: 21718702

Assembly members:

Assembly members:
WT_alpha-synuclein_fibrils, polymer, 140 residues, Formula weight is not available

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: peT28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
WT_alpha-synuclein_fibrils: MDVFMKGKSKAKEGVVAAAE KTKQGVAEAAGKTKEGVLYV GSKTKEGVVHGVATVAEKTK EQVTNVGGAVVTGVTAVAQK TVEGAGSIAAATGFVKKDQL GKNEEGAPQEGILEDMPVDP DNEAYEMPSEEGYQDYEPEA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	246
15N chemical shifts	68

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	alpha synuclein protein	1

Entities:

Entity 1, alpha synuclein protein 140 residues - Formula weight is not available

1	MET	ASP	VAL	PHE	MET	LYS	GLY	LYS	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:

U-13C_15N: WT alpha-synuclein fibrils, [U-13C; U-15N], mM; H2O 100%

2-glycerol_sample: WT alpha-synuclein fibrils, [2-glycerol] 13-C, U-15N, mM; H2O 100%

1_3-glycerol_sample: WT alpha-synuclein fibrils, [1,3-glycerol] 13C, U-15N, mM; H2O 100%

U-13C_15N_doubling_material: WT alpha-synuclein fibrils, [U-13C; U-15N], mM; H2O 100%

sample_conditions_1: pH: 7.5; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
NCACX 50 ms DARR	U-13C_15N	isotropic	sample_conditions_1
NCOCX 50 ms DARR	U-13C_15N	isotropic	sample_conditions_1
NCOCX 250 ms DARR	U-13C_15N	isotropic	sample_conditions_1
CANcoCX 50 ms DARR	U-13C_15N	isotropic	sample_conditions_1
CONcaCX 10 ms DARR	U-13C_15N	isotropic	sample_conditions_1
NCACX 250 ms DARR	2-glycerol_sample	isotropic	sample_conditions_1
NCOCX 250 ms DARR	2-glycerol_sample	isotropic	sample_conditions_1
NCOCX 250 ms DARR	1_3-glycerol_sample	isotropic	sample_conditions_1
CANCO	2-glycerol_sample	isotropic	sample_conditions_1
CANCO	1_3-glycerol_sample	isotropic	sample_conditions_1
NCACX 50 ms DARR	U-13C_15N_doubling_material	isotropic	sample_conditions_1
NCOCX 50 ms DARR	U-13C_15N_doubling_material	isotropic	sample_conditions_1
NCACX 500 ms DARR	2-glycerol_sample	isotropic	sample_conditions_1

Software:

SPARKY v3.115, Goddard - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian UnityPlus 500 MHz
Varian UnityPlus 600 MHz
Varian UnityPlus 600 MHz

BMRB	16300 16302 16342 16543 16546 16547 16548 16904 17214 17498 17648 17649 17654 17665 17910 18207 18208 18243 18857 18860 19257 19337 19338 19344 19345 19350 19351 25227 25228
PDB	1XQ8 2KKW
DBJ	BAF82858 BAG73790
EMBL	CAG33339 CAG46454
GB	AAA16117 AAC02114 AAG30302 AAH13293 AAI08276
REF	NP_000336 NP_001009158 NP_001032222 NP_001129014 NP_001139526
SP	P37840 P61139 P61140 P61142 P61143
AlphaFold	P37840 P61139 P61140 P61142 P61143

1	MET	ASP	VAL	PHE	MET	LYS	GLY	LYS	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	LYS	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