BMRB Entry 34883

Name: NMR solution structure of thyropin IrThy-Cd from the hard tick Ixodes ricinus
Published: 2024-02-26

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PDB ID: 8r6t
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34883
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 thyropin IrThy-Cd from the hard tick Ixodes ricinus

Deposition date:

2023-11-23

Original release date:

2024-02-26

Authors:

Srb, P.; Veverka, V.; Matouskova, Z.; Orsaghova, K.; Mares, M.

Citation:

Citation: Matouskova, Zuzana; Orsaghova, Katarina; Srb, Pavel; Pytelkova, Jana; Kukacka, Zdenek; Busa, Michal; Hajdusek, Ondrej; Sima, Radek; Fabry, Milan; Novak, Petr; Horn, Martin; Kopacek, Petr; Mares, Michael. "An Unusual Two-Domain Thyropin from Tick Saliva: NMR Solution Structure and Highly Selective Inhibition of Cysteine Cathepsins Modulated by Glycosaminoglycans" Int. J. Mol. Sci. 25, 2240-2240 (2024).
PubMed: 38396918

Assembly members:

Assembly members:
entity_1, polymer, 72 residues, 7849.624 Da.

Natural source:

Natural source: Common Name: castor bean tick Taxonomy ID: 34613 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Ixodes ricinus

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAMGKCLAEHHEKSKSTHSQ VGDDIPKCNLASGYYEQMQC NTQQHWCVDPESGTALGERR SGGCTEAARDHC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	218
15N chemical shifts	55
1H chemical shifts	345

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 72 residues - 7849.624 Da.

1

GLY

ALA

MET

GLY

LYS

CYS

LEU

ALA

GLU

HIS

2

HIS

GLU

LYS

SER

LYS

SER

THR

HIS

SER

GLN

3

VAL

GLY

ASP

ILE

PRO

LYS

CYS

ASN

LEU

4

ALA

SER

GLY

TYR

GLU

GLN

MET

GLN

CYS

5

ASN

THR

GLN

HIS

TRP

CYS

VAL

ASP

PRO

6

GLU

SER

GLY

THR

ALA

LEU

GLY

GLU

ARG

7

SER

GLY

CYS

THR

GLU

ALA

ARG

ASP

8

HIS

CYS

Samples:

sample_1: Tyropin, [U-13C; U-15N], 200 uM; sodium chloride 100 mM; TRIS 25 mM

sample_conditions_1: ionic strength: 125 mM; pH: 8.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	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 HNCACO	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRFAM-SPARKY, NMRFAM-SPARKY - chemical shift assignment

NMR spectrometers:

Bruker AVANCE 850 MHz

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