BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19357

Title: Backbone 1H, 13C, 15N chemical shift assignments for the Met66 prodomain region of BDNF   PubMed: 24048383

Deposition date: 2013-07-10 Original release date: 2014-02-10

Authors: Bracken, Clay

Citation: Anastasia, Agustin; Deinhardt, Katrin; Chao, Moses; Will, Nathan; Irmady, Krithi; Lee, Francis; Hempstead, Barbara; Bracken, Clay. "Val66Met polymorphism of BDNF alters prodomain structure to induce neuronal growth cone retraction."  Nat. Commun. 4, 2490-2490 (2013).

Assembly members:
bdnf_prodomain_met66, polymer, 92 residues, 10201.4 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

Entity Sequences (FASTA):
bdnf_prodomain_met66: MEANIRGQGGLAYPGVRTHG TLESVNGPKAGSRGLTSLAD TFEHMIEELLDEDQKVRPNE ENNKDADLYTSRVMLSSQVP LEPPLLFLLEEY

Data sets:
Data typeCount
13C chemical shifts264
15N chemical shifts85
1H chemical shifts85

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1Met66 BDNF Prodomain1

Entities:

Entity 1, Met66 BDNF Prodomain 92 residues - 10201.4 Da.

The first residue (MET 22) is non-native.

1   METGLUALAASNILEARGGLYGLNGLYGLY
2   LEUALATYRPROGLYVALARGTHRHISGLY
3   THRLEUGLUSERVALASNGLYPROLYSALA
4   GLYSERARGGLYLEUTHRSERLEUALAASP
5   THRPHEGLUHISMETILEGLUGLULEULEU
6   ASPGLUASPGLNLYSVALARGPROASNGLU
7   GLUASNASNLYSASPALAASPLEUTYRTHR
8   SERARGVALMETLEUSERSERGLNVALPRO
9   LEUGLUPROPROLEULEUPHELEULEUGLU
10   GLUTYR

Samples:

sample_1: bdnf prodomain, [U-95% 13C; U-95% 15N], 0.1-0.5 mM; sodium chloride 100 mM; sodium phosphate 50 mM; DSS 0.1 mM; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 150 mM; pH: 6.8; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

BMRB 19358
DBJ BAF82452 BAF82542 BAG73983
EMBL CAA42761 CAA62632
GB AAA51820 AAA69805 AAA96140 AAG47511 AAG47512
REF NP_001012443 NP_001137277 NP_001137278 NP_001137279 NP_001137280
SP P23560 Q5IS78

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