BMRB Entry 30951

Name: NMR solution structure of a neurotoxic thionin from Urtica ferox
Published: 2022-07-21

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PDB ID: 7s7p
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30951
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:

NMR solution structure of a neurotoxic thionin from Urtica ferox

Deposition date:

2021-09-16

Original release date:

2022-07-21

Authors:

Durek, T.; Harvey, P.; Craik, D.

Citation:

Citation: Xie, Jing; Robinson, Samuel; Gilding, Edward; Jami, Sina; Deuis, Jennifer; Rehm, Fabian; Yap, Kuok; Ragnarsson, Lotten; Chan, Lai Yue; Hamilton, Brett; Harvey, Peta; Craik, David; Vetter, Irina; Durek, Thomas. "Neurotoxic and cytotoxic peptides underlie the painful stings of the tree nettle Urtica ferox" J. Biol. Chem. 298, 102218-102218 (2022).
PubMed: 35780839

Assembly members:

Assembly members:
entity_1, polymer, 42 residues, 4379.144 Da.

Natural source:

Natural source: Common Name: Urtica ferox Taxonomy ID: 1435581 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Urtica ferox

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KSCCPSTTARNIYNTCRFGG GSRTLCAKLSGCKIVSGTTC PK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	101
15N chemical shifts	33
1H chemical shifts	215

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 42 residues - 4379.144 Da.

1

LYS

SER

CYS

PRO

SER

THR

ALA

ARG

2

ASN

ILE

TYR

ASN

THR

CYS

ARG

PHE

GLY

3

GLY

SER

ARG

THR

LEU

CYS

ALA

LYS

LEU

SER

4

GLY

CYS

LYS

ILE

VAL

SER

GLY

THR

CYS

5

PRO

LYS

Samples:

sample_1: Urthi-1 4.4 ± 0.2 mg/mL

sample_conditions_1: pH: 4.1; pressure: 1 atm; temperature: 298.0 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

CYANA v3.98.13, Guentert - refinement, structure calculation

TopSpin, Bruker Biospin - processing

CcpNmr Analysis, CCPN - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III HD 600 MHz

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