BMRB Entry 34814

Name: TrkB transmembrane domain NMR structure in DMPC/DHPC bicelles
Published: 2024-05-08

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PDB ID: 8oyd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34814
MolProbity Validation Chart

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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:

TrkB transmembrane domain NMR structure in DMPC/DHPC bicelles

Deposition date:

2023-05-04

Original release date:

2024-05-08

Authors:

Kot, E.; Mineev, K.; Goncharuk, S.

Citation:

Citation: Kot, E.; Mineev, K.; Goncharuk, S.; Vilar, M.; Franco, M.; Benito-Martinez, A.. "Structural Basis for the transmembrane signaling and antidepressant-induced activation of the receptor tyrosine kinase TrkB" .

Assembly members:

Assembly members:
entity_1, polymer, 45 residues, 4975.101 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: pGEMEX-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MTDKTGREHLSVYAVVVIAS VVGFCLLVMLFLLKLARHSK FGMKG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	195
15N chemical shifts	45
1H chemical shifts	338

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 45 residues - 4975.101 Da.

1

MET

THR

ASP

LYS

THR

GLY

ARG

GLU

HIS

LEU

2

SER

VAL

TYR

ALA

VAL

ILE

ALA

SER

3

VAL

GLY

PHE

CYS

LEU

VAL

MET

LEU

4

PHE

LEU

LYS

LEU

ALA

ARG

HIS

SER

LYS

5

PHE

GLY

MET

LYS

GLY

Samples:

sample_1: D2O, [U-2H], 5 ± 0.5 % v/v; High affinity receptor of neurotrophin-4 and brain-derived neurotrophic factor (TrkB), [U-100% 13C; U-100% 15N], 1.1 ± 0.05 mM; DMPC, [U-2H], 9.6 ± 0.1 mM; DHPC, [U-2H], 42.7 ± 0.5 mM; TCEP, n.a., 1.0 ± 0.1 mM; sodium azide, n.a., 0.01 ± 0.001 % w/v; sodium phosphate buffer, n.a., 20.0 ± 0.1 mM; TSP, d4, 0.5 ± 0.01 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.0; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	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 HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C-NOESY, 13C-filtered	sample_1	isotropic	sample_conditions_1
1D 1H	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.98.5, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

TopSpin v3.2, Bruker Biospin - collection, processing

CARA v1.9.1.7, Keller and Wuthrich - chemical shift assignment, peak picking

TALOS-N, Shen and Bax - structure calculation

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks