BMRB Entry 26003

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR26003
MolProbity Validation Chart

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Title:
HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE SPIDER VENOM PEPTIDE U3-SCYTOTOXIN-STH1H
Deposition date:
2016-03-18
Original release date:
2016-06-01
Authors:
Loening, Nikolaus
Citation:

Citation: Ariki, Nathanial; Munoz, Lisa; Armitage, Elizabeth; Goodstein, Francesca; George, Kathryn; Smith, Vanessa; Vetter, Irina; Herzig, Volker; King, Glenn; Loening, Nikolaus. "Characterization of Three Venom Peptides from the Spitting Spider Scytodes thoracica"  PLoS One 11, e0156291-e0156291 (2016).
PubMed: 27227898

Assembly members:

Assembly members:
U3-scytotoxin-Sth1h, polymer, 33 residues, 3612.2453 Da.

Natural source:

Natural source:   Common Name: spitting spider   Taxonomy ID: 1112478   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Scytodes thoracica

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PLIC-MBP

Entity Sequences (FASTA):

Entity Sequences (FASTA):
U3-scytotoxin-Sth1h: GLIESIACMQKGLPCMEHVD CCHGVCDSLFCLY

Data typeCount
13C chemical shifts143
15N chemical shifts64
1H chemical shifts444

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1SYTXD 71

Entities:

Entity 1, SYTXD 7 33 residues - 3612.2453 Da.

1   GLYLEUILEGLUSERILEALACYSMETGLN
2   LYSGLYLEUPROCYSMETGLUHISVALASP
3   CYSCYSHISGLYVALCYSASPSERLEUPHE
4   CYSLEUTYR

Samples:

sample_new_2: U3-scytotoxin-Sth1h, [U-13C; U-15N], 0.55 ± 0.10 mM

15N-13C: SYTXD_7, [U-98% 13C; U-98% 15N], 0.4 ± 0.0001 mM

15N: SYTXD_7, [U-98% 13C; U-98% 15N], 0.55 ± 0.0001 mM

sample_new_1: U3-scytotoxin-Sth1h, [U-13C; U-15N], 0.40 ± 0.10 mM

Standard: ionic strength: 0.030 M; pH: 6.500; pressure: 1.000 atm; temperature: 298.000 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC/HMQC15N-13CisotropicStandard
2D 1H-15N HSQC/HMQC15N-13CisotropicStandard
2D 1H-13C HSQC/HMQC15N-13CisotropicStandard
2D 1H-13C HSQC/HMQC15N-13CisotropicStandard
2D 1H-13C HSQC/HMQC15N-13CisotropicStandard
3D HNCO15N-13CisotropicStandard
HNCACO (H[N[ca[CO]]])15N-13CisotropicStandard
HNCOCACB (H[N[co[{CA|ca[C]}]]])15N-13CisotropicStandard
3D HNCACB15N-13CisotropicStandard
2D 1H-1H TOCSY15N-13CisotropicStandard
2D 1H-1H NOESY15N-13CisotropicStandard
3D HCCH-TOCSY15N-13CisotropicStandard
13C HSQC NOESY (H_H[{N|C}].through-space)15N-13CisotropicStandard
13C Aro HSQC NOESY (H_H[{N|C}].through-space)15N-13CisotropicStandard
15N HSQC NOESY (H_H[{N|C}].through-space)15N-13CisotropicStandard
2D 1H-15N HSQC/HMQC15NisotropicStandard
2D 1H-1H TOCSY15NisotropicStandard
2D 1H-1H NOESY15NisotropicStandard
2D 1H-1H NOESY15NisotropicStandard
13C ARO HSQC NOESYsample_new_1solutionStandard
13C AROMATIC HSQCsample_new_1solutionStandard
13C CT-HSQCsample_new_1solutionStandard
13C HSQCsample_new_1solutionStandard
13C HSQC NOESYsample_new_1solutionStandard
15N HMQCsample_new_1solutionStandard
15N HMQC 2sample_new_1solutionStandard
15N HSQC NOESYsample_new_1solutionStandard
1H NOESY (120MS)sample_new_1solutionStandard
1H TOCSYsample_new_1solutionStandard
HCCH TOCSYsample_new_1solutionStandard
HNCACBsample_new_1solutionStandard
HNCACOsample_new_1solutionStandard
HNCOsample_new_1solutionStandard
HNCOCACBsample_new_1solutionStandard
15N HSQC (15N SAMPLE)sample_new_2solutionStandard
1H TOCSY (15N SAMPLE)sample_new_2solutionStandard
NOESY 120MS (15N SAMPLE)sample_new_2solutionStandard
NOESY 200MS (15N SAMPLE)sample_new_2solutionStandard

Software:

ARIA v2.3.2, Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E., Nilges M. - NOE assignment, structure calculation

AutoDep v4.3, PDBe - chemical shift assignment

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - chemical shift assignment

CcpNmr_Analysis v2.4, CCPN - chemical shift assignment, project management

Talos-N v4.12, Yang Shen and Ad Bax - protein backbone dihedral angle prediction

NMR spectrometers:

  • Bruker Avance III 600 MHz
  • Bruker AVANCE 600 MHz

Related Database Links:

ArachnoServer U3-scytotoxin-Sth1h

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