BMRB Entry 52006

Name: Assignment of Lipidic amyloid-b (1-40) fibril
Published: 2024-02-14

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52006

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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:

Assignment of Lipidic amyloid-b (1-40) fibril

Deposition date:

2023-06-20

Original release date:

2024-02-14

Authors:

Frieg, Benedikt; Han, Mookyoung; Giller, Karin; Dienemann, Christian; Riedel, Dietmar; Becker, Stefan; Andreas, Loren; Griesinger, Christian; Schroder, Gunnar

Citation:

Citation: Frieg, Benedikt; Han, Mookyoung; Giller, Karin; Dienemann, Christian; Riedel, Dietmar; Becker, Stefan; Andreas, Loren; Griesinger, Christian; Schroeder, Gunnar. "Cryo-EM structures of lipidic fibrils of amyloid-b (1-40)" Nat. Commun. 15, 1297-1297 (2024).
PubMed: 38351005

Assembly members:

Assembly members:
entity_1, polymer, 40 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: pET32a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: DAEFRHDSGYEVHHQKLVFF AEDVGSNKGAIIGLMVGGVV

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	151
15N chemical shifts	39
1H chemical shifts	41

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	amyloid beta fibril	1

Entities:

Entity 1, amyloid beta fibril 40 residues - Formula weight is not available

1	ASP	ALA	GLU	PHE	ARG	HIS	ASP	SER	GLY	TYR
2	GLU	VAL	HIS	HIS	GLN	LYS	LEU	VAL	PHE	PHE
3	ALA	GLU	ASP	VAL	GLY	SER	ASN	LYS	GLY	ALA
4	ILE	ILE	GLY	LEU	MET	VAL	GLY	GLY	VAL	VAL

Samples:

sample_1: amyloid beta protein (1-40), [U-100% 13C; U-100% 15N], 10 mM; amyloid beta protein (1-40), [U-100% 13C], 10 mM; amyloid beta protein (1-40), [U-13C; U-15N; U-2H], 10 mM

sample_conditions_1: pH: 6.5; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D hCANH	sample_1	isotropic	sample_conditions_1
3D hcoCAcoNH	sample_1	isotropic	sample_conditions_1
3D hCONH	sample_1	isotropic	sample_conditions_1
3D hCOcaNH	sample_1	isotropic	sample_conditions_1
3D hcaCBcaNH	sample_1	isotropic	sample_conditions_1
3D hcaCBcacoNH	sample_1	isotropic	sample_conditions_1
2D 13C-13C DARR	sample_1	isotropic	sample_conditions_1
15N-(1H) NOE	sample_1	isotropic	sample_conditions_1

Software:

CcpNMR - chemical shift assignment, data analysis

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker AVANCE III 850 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	ASP	ALA	GLU	PHE	ARG	HIS	ASP	SER	GLY	TYR
2	GLU	VAL	HIS	HIS	GLN	LYS	LEU	VAL	PHE	PHE
3	ALA	GLU	ASP	VAL	GLY	SER	ASN	LYS	GLY	ALA
4	ILE	ILE	GLY	LEU	MET	VAL	GLY	GLY	VAL	VAL

1	ASP	ALA	GLU	PHE	ARG	HIS	ASP	SER	GLY	TYR
2	GLU	VAL	HIS	HIS	GLN	LYS	LEU	VAL	PHE	PHE
3	ALA	GLU	ASP	VAL	GLY	SER	ASN	LYS	GLY	ALA
4	ILE	ILE	GLY	LEU	MET	VAL	GLY	GLY	VAL	VAL

1	ASP	ALA	GLU	PHE	ARG	HIS	ASP	SER	GLY	TYR
2	GLU	VAL	HIS	HIS	GLN	LYS	LEU	VAL	PHE	PHE
3	ALA	GLU	ASP	VAL	GLY	SER	ASN	LYS	GLY	ALA
4	ILE	ILE	GLY	LEU	MET	VAL	GLY	GLY	VAL	VAL