BMRB Entry 36345

Name: Solution structure of recombinant APETx1
Published: 2020-12-17

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PDB ID: 7bwi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36345
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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:

Solution structure of recombinant APETx1

Deposition date:

2020-04-14

Original release date:

2020-12-17

Authors:

Matsumura, K.; Kobayashi, N.; Kurita, J.; Nishimura, Y.; Yokogawa, M.; Imai, S.; Shimada, I.; Osawa, M.

Citation:

Citation: Matsumura, K.; Shimomura, T.; Kubo, Y.; Kobayashi, N.; Imai, S.; Yanase, N.; Akimoto, M.; Yokogawa, M.; Ikeda, I.; Kurita, J.; Nishimura, Y.; Shimada, I.; Osawa, M.. "Functional characterization for hERG inhibition by sea anemone gating-modifier toxin APETx1" .

Assembly members:

Assembly members:
Kappa-actitoxin-Ael2a, polymer, 42 residues, 4561.226 Da.

Natural source:

Natural source: Common Name: Green aggregating anemone Taxonomy ID: 6110 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Anthopleura elegantissima

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Kappa-actitoxin-Ael2a: GTTCYCGKTIGIYWFGTKTC PSNRGYTGSCGYFLGICCYP VD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	180
15N chemical shifts	40
1H chemical shifts	263

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 42 residues - 4561.226 Da.

1

GLY

THR

CYS

TYR

CYS

GLY

LYS

THR

ILE

2

GLY

ILE

TYR

TRP

PHE

GLY

THR

LYS

THR

CYS

3

PRO

SER

ASN

ARG

GLY

TYR

THR

GLY

SER

CYS

4

GLY

TYR

PHE

LEU

GLY

ILE

CYS

TYR

PRO

5

VAL

ASP

Samples:

sample_1: APETx1, [U-100% 13C; U-100% 15N], 0.691 mM; potassium phosphate 20 mM; sodium chloride 100 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 120 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCACB	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 HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

Amber v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - structure calculation

MAGRO v2.01.28, Kobayashi, N. - data analysis, peak picking

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

NMRView, Johnson, One Moon Scientific - data analysis

Sparky, Goddard - chemical shift assignment

TopSpin v3.5, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE III HD 700 MHz
Bruker Avance 600 600 MHz

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