BMRB Entry 31068

Name: STRUCTURE OF ALPHA-SYNUCLEIN FIBRILS DERIVED FROM HUMAN LEWY BODY DEMENTIA TISSUE
Published: 2023-02-14

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PDB ID: 8fpt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31068
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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:

STRUCTURE OF ALPHA-SYNUCLEIN FIBRILS DERIVED FROM HUMAN LEWY BODY DEMENTIA TISSUE

Deposition date:

2023-01-05

Original release date:

2023-02-14

Authors:

Barclay, A.; Dhavale, D.; Borcik, C.; Rau, M.; Basore, K.; Milchberg, M.; Warmuth, O.; Kotzbauer, P.; Rienstra, C.

Citation:

Citation: Barclay, A.; Dhavale, D.; Borcik, C.; Milchberg, M.; Warmuth, O.; Kotzbauer, P.; Rienstra, C.. "STRUCTURE OF ALPHA-SYNUCLEIN FIBRILS DERIVED FROM HUMAN LEWY BODY DEMENTIA TISSUE" .

Assembly members:

Assembly members:
entity_1, polymer, 140 residues, 14476.108 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 BL21(DE3) Vector: PET28A-AS

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MDVFMKGLSKAKEGVVAAAE KTKQGVAEAAGKTKEGVLYV GSKTKEGVVHGVATVAEKTK EQVTNVGGAVVTGVTAVAQK TVEGAGSIAAATGFVKKDQL GKNEEGAPQEGILEDMPVDP DNEAYEMPSEEGYQDYEPEA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	190
15N chemical shifts	47

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1
3	unit_3	1
4	unit_4	1
5	unit_5	1
6	unit_6	1
7	unit_7	1
8	unit_8	1
9	unit_9	1
10	unit_10	1

Entities:

Entity 1, unit_1 140 residues - 14476.108 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%

sample_2: ALPHA-SYNUCLEIN, [U-100% 2H; U-100% 13C; U-100% 15N], 66%

sample_3: ALPHA-SYNUCLEIN 80%; labelled ALPHA-SYNUCLEIN, [U-25% 2-13C GLYCEROL; U-100% 15N], 20%

sample_conditions_1: ionic strength: 100 mM; pH: 7.6; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D CC DARR	sample_1	isotropic	sample_conditions_1
2D NCO	sample_3	isotropic	sample_conditions_1
2D NCA	sample_3	isotropic	sample_conditions_1
2D CC DARR	sample_3	isotropic	sample_conditions_1
2D CC FPRFDR	sample_2	isotropic	sample_conditions_1
2D CACO CTUC-COSY	sample_2	isotropic	sample_conditions_1
4D HN[HH]NH RFDR	sample_2	isotropic	sample_conditions_1
3D N[HH]NH RFDR	sample_2	isotropic	sample_conditions_1
3D CA[HH]NH RFDR	sample_2	isotropic	sample_conditions_1
3D CAN[H]H RFDR	sample_2	isotropic	sample_conditions_1
3D CO[CA]NH RFDR	sample_2	isotropic	sample_conditions_1
3D CA[CO]NH RFDR	sample_2	isotropic	sample_conditions_1
3D CONH	sample_2	isotropic	sample_conditions_1
3D CANH	sample_2	isotropic	sample_conditions_1
1D C FSREDOR	sample_1	isotropic	sample_conditions_1
3D NCACX PAR	sample_1	isotropic	sample_conditions_1
3D CCC RFDR THEN PAR	sample_1	isotropic	sample_conditions_1
2D CC PAR	sample_1	isotropic	sample_conditions_1
3D CANCO	sample_1	isotropic	sample_conditions_1
3D NCOCA SPC5	sample_1	isotropic	sample_conditions_1
3D NCOCX DARR	sample_1	isotropic	sample_conditions_1
3D NCACX DARR	sample_1	isotropic	sample_conditions_1
2D NCO	sample_1	isotropic	sample_conditions_1
2D NCA	sample_1	isotropic	sample_conditions_1
2D CC DARR	sample_1	isotropic	sample_conditions_1
3D CANCO	sample_1	isotropic	sample_conditions_1
3D NCOCX DARR	sample_1	isotropic	sample_conditions_1
3D NCACX DARR	sample_1	isotropic	sample_conditions_1
2D CC SPC7	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMRFAM-SPARKY, LEE, TONELLI and MARKLEY, LEE, TONELLI, and MARKLEY - chemical shift assignment, peak picking

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

NMR spectrometers:

Agilent VNMRS 750 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