BMRB Entry 34303

Name: Receptor-bound Ghrelin conformation
Published: 2019-07-15

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PDB ID: 6h3e
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34303
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: Receptor-bound Ghrelin conformation PubMed: 31416915

Deposition date: 2018-07-18 Original release date: 2019-07-15

Authors: Ferre, G.; Damian, M.; M'Kadmi, C.; Saurel, O.; Czaplicki, G.; Demange, P.; Marie, J.; Fehrentz, J.; Baneres, J.; Milon, A.

Citation: Ferre, Guillaume; Louet, Maxime; Saurel, Oliver; Delort, Bartholome; Czaplicki, Georges; M'Kadmi, Celine; Damian, Marjorie; Renault, Pedro; Cantel, Sonia; Gavara, Laurent; Demange, Pascal; Marie, Jacky; Fehrentz, Jean-Alain; Floquet, Nicolas; Milon, Alain; Baneres, Jean-Louis. "Structure and dynamics of G protein-coupled receptor-bound ghrelin reveal the critical role of the octanoyl chain" Proc. Natl. Acad. Sci. U.S.A. 116, 17525-17530 (2019).

Assembly members:
entity_1, polymer, 19 residues, 2130.301 Da.
entity_FKZ, non-polymer, 129.243 Da.

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

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GSDFLSPEHQRVQQRKESX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
15N chemical shifts	9
1H chemical shifts	141

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 19 residues - 2130.301 Da.

1

GLY

SER

ASP

PHE

LEU

SER

PRO

GLU

HIS

GLN

2

ARG

VAL

GLN

ARG

LYS

GLU

SER

NH2

Entity 2, entity_2 - C8 H19 N - 129.243 Da.

1

FKZ

Samples:

sample_1: Ghrelin 1-18, [U-15N]-Phe-Leu-Val, 1.37 ± 0.1 mM; Ghrelin receptor, [U-2H], 2.05 ± 0.5 uM; KCl 100 mM

sample_2: Ghrelin 1-18, [U-15N]-Phe-Leu-Val, 1.37 ± 0.1 mM; Ghrelin receptor, [U-2H], 2.05 ± 0.5 uM; JMV5327 2.05 ± 0.5 uM; KCl 100 mM

sample_3: Ghrelin 1-18, [U-15N]-Phe-Leu-Val-Ser-Gln-Glu, 1.15 ± 0.1 mM; Ghrelin receptor, [U-2H], 1.72 ± 0.5 uM; KCl 100 mM

sample_4: Ghrelin 1-18, [U-15N]-Phe-Leu-Val-Ser-Gln-Glu, 1.15 ± 0.1 mM; Ghrelin receptor, [U-2H], 1.72 ± 0.5 uM; JMV5327 1.72 ± 0.5 uM; KCl 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 280 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-1H-15N NOESY-HMQC	sample_3	isotropic	sample_conditions_1
3D 1H-1H-15N NOESY-HMQC	sample_4	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N SOFAST-HMQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N SOFAST-HMQC	sample_4	isotropic	sample_conditions_1

Software:

TOPSPIN v3.5, Bruker Biospin - collection

TOPSPIN v3.2, Bruker Biospin - processing

SPARKY v1.2, T. D. Goddard and D. G. Kneller, SPARKY 3, UCSF - peak picking

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

NMR spectrometers:

Bruker AvanceIII 700 MHz

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