BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 18080

Title: structure of amyloid precursor protein's transmembrane domain

Deposition date: 2011-11-15 Original release date: 2012-01-25

Authors: Nadezhdin, Kirill; Bocharova, Olga; Bocharov, Eduard; Arseniev, Alexander

Citation: Nadezhdin, Kirill; Bocharova, Olga; Bocharov, Eduard; Arseniev, Alexander. "Structural and Dynamic Study of the Transmembrane Domain of the Amyloid Precursor Protein"  Acta Naturae ., .-. (2010).

Assembly members:
entity, polymer, 43 residues, 4450.500 Da.

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   Vector: pGEMEX-1

Entity Sequences (FASTA):
entity: GSQKLVFFAEDVGSNKGAII GLMVGGVVIATVIVITLVML KKK

Data sets:
Data typeCount
13C chemical shifts138
15N chemical shifts44
1H chemical shifts273

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1amyloid precursor protein's transmembrane domain1

Entities:

Entity 1, amyloid precursor protein's transmembrane domain 43 residues - 4450.500 Da.

1   GLYSERGLNLYSLEUVALPHEPHEALAGLU
2   ASPVALGLYSERASNLYSGLYALAILEILE
3   GLYLEUMETVALGLYGLYVALVALILEALA
4   THRVALILEVALILETHRLEUVALMETLEU
5   LYSLYSLYS

Samples:

sample_1: APPjmtm, [U-100% 13C; U-100% 15N], 0.3 – 1 mM; DPC, [U-100% 2H], 21 – 70 mM; H2O 95%; D2O 5%

sample_2: APPjmtm, [U-100% 15N], 0.3 – 1 mM; DPC21 – 70 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 20 mM; pH: 4.6; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - geometry optimization, visualization

TALOS+, Cornilescu, Delaglio and Bax - refinement, structure solution

CARA, R.L.J.Keller - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 15775 18649
PDB
DBJ BAA22264 BAA84580 BAB71958 BAC34997 BAC36369
EMBL CAA30050 CAA30488 CAA31830 CAA39589 CAA39590
GB AAA35540 AAA36829 AAA37139 AAA51722 AAA51726
PIR A60045 D60045 E60045 G60045 JH0773
PRF 1303338A 1403400A 1507304A 1507304B 1507304C
REF NP_000475 NP_001005698 NP_001006601 NP_001013036 NP_001070264
SP O73683 P05067 P08592 P12023 P53601
TPG DAA33655

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