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PDB ID: 9yfc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31269
MolProbity Validation Chart

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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 A30P Alpha-synuclein Fibrils

Deposition date:

2025-09-25

Original release date:

2026-07-29

Authors:

Milchberg, M.; Warmuth, O.; Rienstra, C.

Citation:

Citation: Milchberg, Moses; Warmuth, Owen; Borcik, Collin; Han, Ruixian; Harding, Benjamin; DeZonia, Barry; Dhavale, Dhruva; Pierson, Joshua; Kotzbauer, Paul; Wright, Elizabeth; Schwieters, Charles; Rienstra, Chad. "In Vitro-Prepared A30P Alpha-Synuclein Fibrils Adopt the Conserved and Disease-Relevant Greek Key Fold " J. Phys. Chem. B 130, 7120-7133 (2026).
PubMed: 42389901

Assembly members:

Assembly members:
entity_1, polymer, 140 residues, 14502.146 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 KTKQGVAEAPGKTKEGVLYV GSKTKEGVVHGVATVAEKTK EQVTNVGGAVVTGVTAVAQK TVEGAGSIAAATGFVKKDQL GKNEEGAPQEGILEDMPVDP DNEAYEMPSEEGYQDYEPEA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	259
15N chemical shifts	67

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

Entities:

Entity 1, unit_1 140 residues - 14502.146 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	PRO
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], 1 mM; sodium phosphate 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 13C CP	sample_1	isotropic	sample_conditions_1
1D 13C DP	sample_1	isotropic	sample_conditions_1
1D 15N CP	sample_1	isotropic	sample_conditions_1
1D 15N DP	sample_1	isotropic	sample_conditions_1
2D 13C-13C DARR 50 ms	sample_1	isotropic	sample_conditions_1
3D 13C-13C-13C DARR 50, 500 ms	sample_1	isotropic	sample_conditions_1
3D 13C-13C-13C DARR 50, 500 ms	sample_1	isotropic	sample_conditions_1
3D 13CA-15N-{13CO}-13CX DARR 50 ms	sample_1	isotropic	sample_conditions_1
3D 13CA-15N-13CO	sample_1	isotropic	sample_conditions_1
3D 15N-13CO-13CX DARR 50 ms	sample_1	isotropic	sample_conditions_1
3D 15N-13CA-13CX DARR 50 ms	sample_1	isotropic	sample_conditions_1
2D 15N-{13CA}-13CX DARR 50 ms	sample_1	isotropic	sample_conditions_1
2D 15N-13CA	sample_1	isotropic	sample_conditions_1
2D 13C-13C DARR 500 ms	sample_1	isotropic	sample_conditions_1
2D 13C-13C DARR 125 ms	sample_1	isotropic	sample_conditions_1

Software:

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

X-PLOR NIH v3.66, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMRFAM-SPARKY v3.196, Lee, Tonelli, Markley - chemical shift assignment, peak picking

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

VnmrJ vOVJ 3, Varian - collection

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

NMR spectrometers:

Varian VNMRS 750 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	PRO
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	PRO
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

BMRB Entry 31269