BMRB Entry 31058

Title:
Alpha7 nicotinic acetylcholine receptor intracellular and transmembrane domains bound to ivermectin in a desensitized state
Deposition date:
2022-11-11
Original release date:
2023-02-14
Authors:
Bondarenko, V.; Chen, Q.; Tang, P.
Citation:

Citation: Bondarenko, Vasyl; Chen, Qiang; Singewald, Kevin; Haloi, Nandan; Tillman, Tommy; Howard, Rebecca; Lindahl, Erik; Xu, Yan; Tang, Pei. "Structural Elucidation of Ivermectin Binding to Alpha7nAChR and the Induced Channel Desensitization"  ACS Chem. Neurosci. 14, 1156-1165 (2023).
PubMed: 36821490

Assembly members:

Assembly members:
entity_1, polymer, 272 residues, 29831.779 Da.
entity_IVM, non-polymer, 875.093 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pTBSG1-TMD+ICD

Data sets:
Data typeCount
13C chemical shifts764
15N chemical shifts239
1H chemical shifts1104

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_21
3unit_31
4unit_41
5unit_51
6unit_62
7unit_72
8unit_82
9unit_92
10unit_102

Entities:

Entity 1, unit_1 272 residues - 29831.779 Da.

1   SERASNALAGLUGLUGLULEUTYRTYRGLY
2   LEUASNLEULEUILEPROCYSVALLEUILE
3   SERALALEUALALEULEUVALPHELEULEU
4   PROALAASPSERGLYGLULYSILESERLEU
5   GLYILETHRVALLEULEUSERLEUTHRVAL
6   PHEMETLEULEUVALALAGLUILEMETPRO
7   SERTHRSERASPSERSERPROSERILEALA
8   GLNTYRPHEALASERTHRMETILEILEVAL
9   GLYLEUSERVALVALVALTHRVALILEVAL
10   LEUGLNTYRHISHISHISASPPROASPGLY
11   GLYLYSMETPROLYSTRPTHRARGVALILE
12   LEULEUASNTRPCYSALATRPPHELEUARG
13   METLYSARGPROGLYGLUASPLYSVALARG
14   PROALACYSGLNHISLYSGLNARGARGCYS
15   SERLEUALASERVALGLUMETSERALAVAL
16   ALAPROPROPROALASERASNGLYASNLEU
17   LEUTYRILEGLYPHEARGGLYLEUASPGLY
18   VALHISCYSVALPROTHRPROASPSERGLY
19   VALVALCYSGLYARGMETALACYSSERPRO
20   THRHISASPGLUHISLEULEUHISGLYGLY
21   GLNPROPROGLUGLYASPPROASPLEUALA
22   LYSILELEUGLUGLUVALARGTYRILEALA
23   ASNARGPHEARGCYSGLNASPGLUSERGLU
24   ALAVALCYSSERGLUTRPLYSPHEALAALA
25   CYSVALVALASPARGLEUCYSLEUMETALA
26   PHESERVALPHETHRILEILECYSTHRILE
27   GLYILELEUMETSERALAPROASNPHEVAL
28   GLUGLU

Entity 2, unit_6 - C48 H74 O14 - 875.093 Da.

1   IVM

Samples:

sample_1: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM

sample_2: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 30 uM; DMSO 0.1%

sample_3: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 100 uM; DMSO 0.3%

sample_4: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 250 uM; DMSO 0.55%

sample_5: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.95%

sample_6: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.8%

sample_7: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.8%

sample_8: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.8%

sample_9: alpha7nAChR C317 TMD+ICD, [U-15N], 0.20 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.8%

sample_10: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 220 uM; DMSO 0.4%; V311C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.22 ± 0.01 mM

sample_11: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; V311C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.22 ± 0.01 mM

sample_12: sodium acetate 5 mM; LDAO 26 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 220 uM; DMSO 0.4%; C335-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.22 ± 0.01 mM

sample_13: sodium acetate 5 mM; LDAO 26 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C335-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.22 ± 0.01 mM

sample_14: sodium acetate 5 mM; LDAO 26 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 200 uM; DMSO 0.4%; C342-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_15: sodium acetate 5 mM; LDAO 26 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C342-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 %

sample_16: sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 200 uM; DMSO 0.4%; S350C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_17: sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; S350C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_18: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 200 uM; DMSO 0.4%; C375-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_19: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C375-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_20: sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 250 uM; DMSO 0.4%; C390-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.25 ± 0.01 mM

sample_21: sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C390-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.25 ± 0.01 mM

sample_22: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 240 uM; DMSO 0.4%; L415C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.24 ± 0.01 mM

sample_23: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; L415C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.24 ± 0.01 mM

sample_24: sodium acetate 5 mM; LDAO 22 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 200 uM; DMSO 0.4%; C435-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_25: sodium acetate 5 mM; LDAO 22 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C435-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_26: alpha7nAChR C317 TMD+ICD, [U-13C; U-15N], 0.22 ± 0.01 mM; sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 30 uM; DMSO 0.2%; PNU 30 uM

sample_27: alpha7nAChR C317 TMD+ICD, [U-13C; U-15N], 0.22 ± 0.01 mM; sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM

sample_conditions_1: ionic strength: 25 mM; pH: 4.7; pressure: 1 atm; temperature: 318 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSY-HSQCsample_1isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_2isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_3isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_4isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_5isotropicsample_conditions_1
2D 1H-15N STD TROSY-HSQCsample_6isotropicsample_conditions_1
2D 1H-15N STD TROSY-HSQCsample_7isotropicsample_conditions_1
2D 1H-15N STD TROSY-HSQCsample_8isotropicsample_conditions_1
2D NOESYsample_9isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_10isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_11isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_12isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_13isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_14isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_15isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_16isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_17isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_18isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_19isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_20isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_21isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_22isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_23isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_24isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_25isotropicsample_conditions_1
3D TROSY-HNCOsample_26isotropicsample_conditions_1
3D TROSY-HNCOsample_27isotropicsample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection

NMRPipe v10.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Sparky v3.190, Goddard - data analysis

NMRFAM-SPARKY v1.470, Lee, Tonelli and Markley - data analysis

CS-ROSETTA v3.17, Shen, Vernon, Baker and Bax - structure calculation

Rosetta v3.7, Rosetta - refinement, structure calculation

MolProbity, Richardson - refinement

NMR spectrometers:

  • Bruker AVANCE II 800 MHz

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