BMRB Entry 17159

Name: Backbone assignment of the affibody-bound amyloid B-peptide
Published: 2010-09-16

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17159

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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 assignment of the affibody-bound amyloid B-peptide PubMed: 20886513

Deposition date: 2010-08-31 Original release date: 2010-09-16

Authors: Lindgren, Joel; Wahlstrom, Anna; Danielsson, Jens; Markova, Natalia; Ekblad, Caroline; Graslund, Astrid; Abrahmsen, Lars; Karlstrom, Amelie; Warmlander, Sebastian

Citation: Lindgren, Joel; Wahlstrom, Anna; Danielsson, Jens; Markova, Natalia; Ekblad, Caroline; Graslund, Astrid; Abrahmsen, Lars; Karlstrom, Amelie Eriksson; Warmlander, Sebastian K T S. "N-terminal engineering of amyloid--binding Affibody molecules yields improved chemical synthesis and higher binding affinity." Protein Sci. 19, 2319-2329 (2010).

Assembly members:
Amyloid_beta-Peptide, polymer, 40 residues, Formula weight is not available

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
Amyloid_beta-Peptide: DAEFRHDSGYEVHHQKLVFF AEDVGSNKGAIIGLMVGGVV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	70
15N chemical shifts	35
1H chemical shifts	35

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

Entities:

Entity 1, Amyloid beta-Peptide 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-Peptide, [U-13C; U-15N], 0.29 ± 0.03 mM; sodium phosphate 10 ± 1 mM; DSS 0.1 ± 0.02 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 10 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HCACO	sample_1	isotropic	sample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 700 MHz

Related Database Links:

BMRB	11435 15775 17186 17764 17793 17794 17795 17796 18052 18127 18128 18129 18131 19009 19309 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

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts

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