BMRB Entry 19358

Name: Backbone 1H, 13C, 15N chemical shift assignments for the Val66 prodomain region of BDNF
Published: 2014-02-10

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19358

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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 1H, 13C, 15N chemical shift assignments for the Val66 prodomain region of BDNF

Deposition date:

2013-07-10

Original release date:

2014-02-10

Authors:

Bracken, Clay

Citation:

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).
PubMed: 24048383

Assembly members:

Assembly members:
bdnf_prodomain_Val66, polymer, 92 residues, 10169.3 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: recombinant technology Host organism: Escherichia coli Vector: pET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
bdnf_prodomain_Val66: MEANIRGQGGLAYPGVRTHG TLESVNGPKAGSRGLTSLAD TFEHVIEELLDEDQKVRPNE ENNKDADLYTSRVMLSSQVP LEPPLLFLLEEY

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	263
15N chemical shifts	85
1H chemical shifts	85

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Val66 BDNF Prodomain	1

Entities:

Entity 1, Val66 BDNF Prodomain 92 residues - 10169.3 Da.

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

1

MET

GLU

ALA

ASN

ILE

ARG

GLY

GLN

GLY

2

LEU

ALA

TYR

PRO

GLY

VAL

ARG

THR

HIS

GLY

3

THR

LEU

GLU

SER

VAL

ASN

GLY

PRO

LYS

ALA

4

GLY

SER

ARG

GLY

LEU

THR

SER

LEU

ALA

ASP

5

THR

PHE

GLU

HIS

VAL

ILE

GLU

LEU

6

ASP

GLU

ASP

GLN

LYS

VAL

ARG

PRO

ASN

GLU

7

GLU

ASN

LYS

ASP

ALA

ASP

LEU

TYR

THR

8

SER

ARG

VAL

MET

LEU

SER

GLN

VAL

PRO

9

LEU

GLU

PRO

LEU

PHE

LEU

GLU

10

GLU

TYR

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:

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

BMRB	19357
DBJ	BAF82452 BAF82542 BAG73983
EMBL	CAA42761 CAA62632
GB	AAA51820 AAA69805 AAA96140 AAB71654 AAD10844
REF	NP_001012443 NP_001137277 NP_001137278 NP_001137279 NP_001137280
SP	O18755 P23560 Q4L0Y3 Q5IS78 Q6LCI5
AlphaFold	O18755 P23560 Q4L0Y3 Q5IS78 Q6LCI5