BMRB Entry 26002

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26002
MolProbity Validation Chart

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Title:
HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE SPIDER VENOM PEPTIDE U3-SCYTOTOXIN-STH1A
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-Sth1a, polymer, 32 residues, 3451.0273 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-Sth1a: GLIESIACIQKGLPCMEHSD CCRGVCEALFCQ

Data typeCount
13C chemical shifts135
15N chemical shifts32
1H chemical shifts212

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1SYTXD 11

Entities:

Entity 1, SYTXD 1 32 residues - 3451.0273 Da.

1   GLYLEUILEGLUSERILEALACYSILEGLN
2   LYSGLYLEUPROCYSMETGLUHISSERASP
3   CYSCYSARGGLYVALCYSGLUALALEUPHE
4   CYSGLN

Samples:

sample_new_2: U3-scytotoxin-Sth1a, [U-13C; U-15N], 0.60 ± 0.10 mM

13C-15N: SYTXD_1, [U-98% 13C; U-98% 15N], 0.55 ± 0.0001 mM

15N: SYTXD_1, [U-98% 13C; U-98% 15N], 0.6 ± 0.0001 mM

sample_new_1: U3-scytotoxin-Sth1a, [U-13C; U-15N], 0.55 ± 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/HMQC13C-15NisotropicStandard
2D 1H-13C HSQC/HMQC13C-15NisotropicStandard
2D 1H-13C HSQC/HMQC13C-15NisotropicStandard
2D 1H-13C HSQC/HMQC13C-15NisotropicStandard
3D HNCO13C-15NisotropicStandard
HNCACO (H[N[ca[CO]]])13C-15NisotropicStandard
HNCOCACB (H[N[co[{CA|ca[C]}]]])13C-15NisotropicStandard
3D HNCACB13C-15NisotropicStandard
3D HCCH-TOCSY13C-15NisotropicStandard
2D 1H-1H TOCSY15NisotropicStandard
2D 1H-1H NOESY15NisotropicStandard
3D 1H-15N TOCSY15NisotropicStandard
2D 1H-15N HSQC/HMQC15NisotropicStandard
13C NOESY 160ms (H_H[{N|C}].through-space)13C-15NisotropicStandard
15N NOESY 160ms (H_H[{N|C}].through-space)13C-15NisotropicStandard
13C Aro NOESY 160ms (H_H[{N|C}].through-space)13C-15NisotropicStandard
13C ARO NOESY 160MSsample_new_1solutionStandard
13C AROMATIC HSQCsample_new_1solutionStandard
13C CT-HSQCsample_new_1solutionStandard
13C HSQCsample_new_1solutionStandard
13C NOESY 160MSsample_new_1solutionStandard
15N HMQC2sample_new_1solutionStandard
15N NOESY 160MSsample_new_1solutionStandard
HCCH TOCSYsample_new_1solutionStandard
HNCACBsample_new_1solutionStandard
HNCACOsample_new_1solutionStandard
HNCOsample_new_1solutionStandard
HNCOCACBsample_new_1solutionStandard
15N HMQCsample_new_2solutionStandard
15N HSQC-TOCSYsample_new_2solutionStandard
1H NOESY (200MS)sample_new_2solutionStandard
1H TOCSYsample_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-Sth1a

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