BMRB Entry 19309

Name: 3D NMR structure of a complex between the amyloid beta peptide (1-40) and the polyphenol epsilon-viniferin glucoside
Published: 2013-09-10

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PDB ID: 2m9r
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19309
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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:

3D NMR structure of a complex between the amyloid beta peptide (1-40) and the polyphenol epsilon-viniferin glucoside

Deposition date:

2013-06-19

Original release date:

2013-09-10

Authors:

Monti, Jean-Pierre; Richard, Tristan

Citation:

Citation: Richard, Tristan; Papastamoulis, Yorgos; Pierre, Waffo-Teguo; Monti, Jean-Pierre. "3D NMR structure of a complex between the amyloid beta peptide (1-40) and the polyphenol epsilon-viniferin glucoside: Implications in Alzheimer's disease" Biochim. Biophys. Acta 1830, 5068-5074 (2013).
PubMed: 23830862

Assembly members:

Assembly members:
amyloid_peptide, polymer, 40 residues, 4335.893 Da.
furan-2-sulfonamide, non-polymer, 147.152 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: chemical synthesis Host organism: human

Entity Sequences (FASTA):

Entity Sequences (FASTA):
amyloid_peptide: DAEFRHDSGYEVHHQKLVFF AEDVGSNKGAIIGLMVGGVV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	268

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	amyloid beta peptide	1
2	EVG_1	2
3	EVG_2	2
4	EVG_3	2
5	EVG_4	2
6	EVG_5	2
7	EVG_6	2
8	EVG_7	2
9	EVG_8	2
10	EVG_9	2
11	EVG_10	2
12	EVG_11	2
13	EVG_12	2

Entities:

Entity 1, amyloid beta peptide 40 residues - 4335.893 Da.

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

Entity 2, EVG_1 - C4 H5 N O3 S - 147.152 Da.

1

EVG

Samples:

sample_1: amyloid peptide 1 mM

sample_conditions_1: pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

InsightII, Accelrys Software Inc. - structure solution

NMR spectrometers:

Bruker Avance 600 MHz

Related Database Links:

BMRB	11435 15775 17159 17186 17764 17793 17794 17795 17796 18052 18127 18128 18129 18131 19009 19393 25218 25289 25429 26508 26516
PDB	1AMB 1AMC 1AML 1BA4 1BA6 1HZ3 1IYT 1Z0Q 2BEG 2G47 2LFM 2LMN 2LMO 2LMP 2LMQ 2LNQ 2LP1 2M4J 2M9R 2M9S 2MVX 2MXU 2OTK 2WK3 3BAE 3IFN 4HIX 4M1C 4MVI 4MVL 4NGE 4ONG 5AEF
DBJ	BAA22264 BAA84580 BAB71958 BAD51938 BAE01907
EMBL	CAA30050 CAA31830 CAA39589 CAA39590 CAA39591
GB	AAA35540 AAA36829 AAA51564 AAA51722 AAA51726
PIR	A60045 D60045 E60045 G60045 PQ0438
PRF	1303338A 1403400A 1405204A 1507304A 1507304B
REF	NP_000475 NP_001006601 NP_001013036 NP_001070264 NP_001127014
SP	P05067 P53601 P79307 P86906 Q28053
TPG	DAA33655
AlphaFold	P05067 P53601 P79307 P86906 Q28053

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