BMRB Entry 34209

Name: Backbone structure of Des-Arg10-Kallidin (DAKD) peptide bound to human Bradykinin 1 Receptor (B1R) determined by DNP-enhanced MAS SSNMR
Published: 2018-01-05

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PDB ID: 6f3y
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34209
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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 structure of Des-Arg10-Kallidin (DAKD) peptide bound to human Bradykinin 1 Receptor (B1R) determined by DNP-enhanced MAS SSNMR

Deposition date:

2017-11-29

Original release date:

2018-01-05

Authors:

Mao, J.; Kuenze, G.; Joedicke, L.; Meiler, J.; Michel, H.; Glaubitz, C.

Citation:

Citation: Joedicke, Lisa; Mao, Jiafei; Kuenze, Georg; Reinhart, Christoph; Kalavacherla, Tejaswi; Jonker, Hendrik; Richter, Christian; Schwalbe, Harald; Meiler, Jens; Preu, Julia; Michel, Hartmut; Glaubitz, Clemens. "The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors." Nat. Chem. Biol. 14, 284-290 (2018).
PubMed: 29334381

Assembly members:

Assembly members:
entity_1, polymer, 9 residues, 1034.210 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: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KRPPGFSPF

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	25
15N chemical shifts	8

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 9 residues - 1034.210 Da.

1

LYS

ARG

PRO

GLY

PHE

SER

PRO

PHE

Samples:

sample_4: Des-Arg10-Kallidin (DAKD), [U-13C; U-15N] P4, 312.5 ± 27.5 uM; human B1R 312.5 ± 27.5 uM; AMUPOL 10 ± 0.3 mM; HEPES 50 mM; NaCl 150 mM; DDM 4 % w/v; CHS 0.4 % w/v

sample_5: Des-Arg10-Kallidin (DAKD), [U-13C; U-15N] G5F6, 312.5 ± 27.5 uM; human B1R 312.5 ± 27.5 uM; AMUPOL 10 ± 0.3 mM; HEPES 50 mM; NaCl 150 mM; DDM 4 % w/v; CHS 0.4 % w/v

sample_6: Des-Arg10-Kallidin (DAKD), [U-13C; U-15N] S7P9, 312.5 ± 27.5 uM; human B1R 312.5 ± 27.5 uM; AMUPOL 10 ± 0.3 mM; HEPES 50 mM; NaCl 150 mM; DDM 4 % w/v; CHS 0.4 % w/v

sample_1: Des-Arg10-Kallidin (DAKD), [U-13C; U-15N] K1, 312.5 ± 27.5 uM; human B1R 312.5 ± 27.5 uM; AMUPOL 10 ± 0.3 mM; HEPES 50 mM; NaCl 150 mM; DDM 4 % w/v; CHS 0.4 % w/v

sample_2: Des-Arg10-Kallidin (DAKD), [U-13C; U-15N] R2S7, 312.5 ± 27.5 uM; human B1R 312.5 ± 27.5 uM; AMUPOL 10 ± 0.3 mM; HEPES 50 mM; NaCl 150 mM; DDM 4 % w/v; CHS 0.4 % w/v

sample_3: Des-Arg10-Kallidin (DAKD), [U-13C; U-15N] P3, 312.5 ± 27.5 uM; human B1R 312.5 ± 27.5 uM; AMUPOL 10 ± 0.3 mM; HEPES 50 mM; NaCl 150 mM; DDM 4 % w/v; CHS 0.4 % w/v

sample_conditions_1: ionic strength: 175 mM; pH: 7.6; pressure: 1 atm; temperature: 110 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 13C-13C DQ-SQ	sample_1	isotropic	sample_conditions_1
2D 15N-13C TEDOR	sample_1	isotropic	sample_conditions_1
2D 13C-13C DQ-SQ	sample_2	isotropic	sample_conditions_1
2D 15N-13C TEDOR	sample_2	isotropic	sample_conditions_1
2D 13C-13C DQ-SQ	sample_3	isotropic	sample_conditions_1
2D 13C-13C DQ-SQ	sample_5	isotropic	sample_conditions_1
2D 15N-13C TEDOR	sample_4	isotropic	sample_conditions_1
2D 13C-13C DQ-SQ	sample_4	isotropic	sample_conditions_1
2D 15N-13C TEDOR	sample_3	isotropic	sample_conditions_1
2D 15N-13C TEDOR	sample_5	isotropic	sample_conditions_1
2D 13C-13C DQ-SQ	sample_6	isotropic	sample_conditions_1
1D REDOR/DQF double-filter 13C	sample_6	isotropic	sample_conditions_1
2D 13C-13C DQ-SQ	sample_6	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure calculation

TOPSPIN, Bruker Biospin - chemical shift assignment, collection, data analysis, processing

CYANA, Guntert, Mumenthaler and Wuthrich - refinement

TALOS-N, Shen, Bax - refinement

PREDITOR, Berjanskii, Neal, Wishart - refinement

flexible-meccano, Ozone, Bauer, Salmon, Huang, Jensen, Segard, Bernado, Charavay, Blackledge - refinement

SHIFTX v1.1, Neal, Nip, Zhang, Wishart - refinement

CIRCOS v0.69.3, Krzywinski, Schein, Birol, Connors, Gascoyne, Horsman, Jones, A Marra - refinement

TALOS+, Shen, Delaglio, Cornilescu, Bax - data analysis

NMR spectrometers:

Bruker AvanceII 400.197 MHz