BMRB Entry 16342

Name: Backbone 1H, 13C, 15N and 13C-beta Chemical Shift Assignments for alpha-synuclein at pH 3
Published: 2009-07-06

Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16342

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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:

Backbone 1H, 13C, 15N and 13C-beta Chemical Shift Assignments for alpha-synuclein at pH 3

Deposition date:

2009-06-09

Original release date:

2009-07-06

Authors:

Cho, Min-Kyu; Kim, Hai-Young; Zweckstetter, Markus

Citation:

Citation: Cho, Min-Kyu; Nodet, Gabrielle; Kim, Hai-Young; Jensen, Malene; Bernado, Pau; Fernandez, Claudio; Becker, Stefan; Blackledge, Martin; Zweckstetter, Markus. "Structural characterization of alpha-synuclein in an aggregation prone state" Protein Sci. 18, 1840-1846 (2009).
PubMed: 19554627

Assembly members:

Assembly members:
human_a-synuclein, polymer, 140 residues, Formula weight is not available

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: T7

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
RDCs
- RDC_list_1

Data type	Count
13C chemical shifts	210
15N chemical shifts	130
1H chemical shifts	130
heteronuclear NOE values	128
residual dipolar couplings	117

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	human a-synuclein	1

Entities:

Entity 1, human a-synuclein 140 residues - Formula weight is not available

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: a-synuclein, [U-13C; U-15N], 300 uM; sodium chloride 100 mM; sodium acetate 20 mM; H2O 90%; D2O 10%

pH3: ionic strength: 0.28 M; pH: 3.0; pressure: 1 atm; temperature: 288 K

pH3_anisotropic: ionic strength: 0.28 M; pH: 3.0; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	pH3
3D CBCA(CO)NH	sample_1	isotropic	pH3
3D HNCACB	sample_1	isotropic	pH3
2D Heteronuclear NOE	sample_1	isotropic	pH3
2D IPAP 1H-15N HSQC	sample_1	anisotropic	pH3_anisotropic
2D 1H-15N R1rho	sample_1	isotropic	pH3
2D 1H-15N R2	sample_1	isotropic	pH3

Software:

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

TOPSPIN v2.1, Bruker Biospin - collection

SPARKY v3.110, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz

BMRB	16300 16302 16543 16546 16547 16548 16904 16939 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	BAB29375 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	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