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- PDB-8f4v: Alpha7 nicotinic acetylcholine receptor intracellular and transme... -

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Basic information

Entry
Database: PDB / ID: 8f4v
TitleAlpha7 nicotinic acetylcholine receptor intracellular and transmembrane domains bound to ivermectin in a desensitized state
ComponentsNeuronal acetylcholine receptor subunit alpha-7
KeywordsMEMBRANE PROTEIN / nicotinic acetylcholine receptor / transmembrane and intracellular domain / desensitized state / ivermectin
Function / homology
Function and homology information


sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / acetylcholine receptor activity / dendritic spine organization ...sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / acetylcholine receptor activity / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / acetylcholine-gated monoatomic cation-selective channel activity / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / plasma membrane raft / modulation of excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / response to amyloid-beta / negative regulation of tumor necrosis factor production / toxic substance binding / monoatomic ion transport / monoatomic ion transmembrane transport / positive regulation of protein metabolic process / positive regulation of long-term synaptic potentiation / synapse organization / response to nicotine / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / monoatomic ion channel activity / amyloid-beta binding / postsynapse / postsynaptic membrane / positive regulation of MAPK cascade / learning or memory / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / neuron projection / positive regulation of protein phosphorylation / synapse / positive regulation of cell population proliferation / signal transduction / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Chem-IVM / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / na
AuthorsBondarenko, V. / Chen, Q. / Tang, P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA046939 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)T32GM075770 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)T32EB009403 United States
CitationJournal: Acs Chem Neurosci / Year: 2023
Title: Structural Elucidation of Ivermectin Binding to alpha 7nAChR and the Induced Channel Desensitization.
Authors: Bondarenko, V. / Chen, Q. / Singewald, K. / Haloi, N. / Tillman, T.S. / Howard, R.J. / Lindahl, E. / Xu, Y. / Tang, P.
History
DepositionNov 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuronal acetylcholine receptor subunit alpha-7
B: Neuronal acetylcholine receptor subunit alpha-7
C: Neuronal acetylcholine receptor subunit alpha-7
D: Neuronal acetylcholine receptor subunit alpha-7
E: Neuronal acetylcholine receptor subunit alpha-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,53410
Polymers149,1595
Non-polymers4,3755
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21370 Å2
ΔGint-157 kcal/mol
Surface area80780 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Neuronal acetylcholine receptor subunit alpha-7


Mass: 29831.779 Da / Num. of mol.: 5
Fragment: Transmembrane domain and intracellular domain residues 231-496
Mutation: A263S, V268S, L270S, A474E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA7, NACHRA7 / Plasmid: pTBSG1-TMD+ICD / Cell (production host): E. coli / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) pLysS / References: UniProt: P36544
#2: Chemical
ChemComp-IVM / (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside / 22,23-DIHYDROAVERMECTIN B1A / IVERMECTIN


Mass: 875.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C48H74O14 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiparasitic*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N TROSY-HSQC
122isotropic12D 1H-15N TROSY-HSQC
133isotropic12D 1H-15N TROSY-HSQC
144isotropic12D 1H-15N TROSY-HSQC
155isotropic12D 1H-15N TROSY-HSQC
166isotropic12D 1H-15N STD TROSY-HSQC
177isotropic12D 1H-15N STD TROSY-HSQC
188isotropic12D 1H-15N STD TROSY-HSQC
199isotropic12D NOESY
11010isotropic12D 1H-15N TROSY-HSQC
11111isotropic12D 1H-15N TROSY-HSQC
11212isotropic12D 1H-15N TROSY-HSQC
11313isotropic12D 1H-15N TROSY-HSQC
11414isotropic12D 1H-15N TROSY-HSQC
11515isotropic12D 1H-15N TROSY-HSQC
11616isotropic12D 1H-15N TROSY-HSQC
11717isotropic12D 1H-15N TROSY-HSQC
11818isotropic12D 1H-15N TROSY-HSQC
11919isotropic12D 1H-15N TROSY-HSQC
12020isotropic12D 1H-15N TROSY-HSQC
12121isotropic12D 1H-15N TROSY-HSQC
12222isotropic12D 1H-15N TROSY-HSQC
12323isotropic12D 1H-15N TROSY-HSQC
12424isotropic12D 1H-15N TROSY-HSQC
12525isotropic12D 1H-15N TROSY-HSQC
12626isotropic13D TROSY-HNCO
12727isotropic13D TROSY-HNCO

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle10.25 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for titration NMR experiments by ivermectin. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_195% H2O/5% D2O
micelle20.25 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 30 uM ivermectin, 0.1 % DMSO, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for titration NMR experiments by ivermectin. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_295% H2O/5% D2O
micelle30.25 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 100 uM ivermectin, 0.3 % DMSO, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for titration NMR experiments by ivermectin. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_395% H2O/5% D2O
micelle40.25 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 250 uM ivermectin, 0.55 % DMSO, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for titration NMR experiments by ivermectin. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_495% H2O/5% D2O
micelle50.25 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 500 uM ivermectin, 0.95 % DMSO, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for titration NMR experiments by ivermectin. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_595% H2O/5% D2O
micelle60.25 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 500 uM ivermectin, 0.8 % DMSO, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for 1D and STD NMR experiments (saturation of ivermectin peaks C1''H/C3H). Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_695% H2O/5% D2O
micelle70.25 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 500 uM ivermectin, 0.8 % DMSO, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for 1D and STD NMR experiments (saturation of ivermectin peak C11H). Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_795% H2O/5% D2O
micelle80.25 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 500 uM ivermectin, 0.8 % DMSO, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for 1D and STD NMR experiments (saturation of ivermectin peak C15H). Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_895% H2O/5% D2O
micelle90.20 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 500 uM ivermectin, 0.8 % DMSO, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for 2D NOESY NMR experiments (mixing time: 120 and 200 ms). Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_995% H2O/5% D2O
micelle100.22 mM [U-15N] V311C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 220 uM ivermectin, 0.4 % DMSO, 95% H2O/5% D2O15N-labeled, single-cysteine V311C-MTSL-labeled alpha7 TMD+ICD with 0- and 2.2-mM ascorbic acid for PRE NMR (0.22 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_V311C-MTSL_1095% H2O/5% D2O
micelle110.22 mM [U-15N] V311C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine V311C-MTSL-labeled alpha7 TMD+ICD with 0- and 2.2-mM ascorbic acid for PRE NMR (0 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_V311C-MTSL_1195% H2O/5% D2O
micelle120.22 mM [U-15N] C335-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 26 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 220 uM ivermectin, 0.4 % DMSO, 95% H2O/5% D2O15N-labeled, single-cysteine C335-MTSL-labeled alpha7 TMD+ICD with 0- and 2.2-mM ascorbic acid for PRE NMR (0.22 mM ivermectin). Additional mutations include C219A, C317S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C335-MTSL_1295% H2O/5% D2O
micelle130.22 mM [U-15N] C335-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 26 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C335-MTSL-labeled alpha7 TMD+ICD with 0- and 2.2-mM ascorbic acid for PRE NMR (0 mM ivermectin). Additional mutations include C219A, C317S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C335-MTSL_1395% H2O/5% D2O
micelle140.2 mM [U-15N] C342-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 26 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 200 uM ivermectin, 0.4 % DMSO, 95% H2O/5% D2O15N-labeled, single-cysteine C342-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0.2 mM ivermectin). Additional mutations include C219A, C317S, C335S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C342-MTSL_1495% H2O/5% D2O
micelle150.2 % [U-15N] C342-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 26 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C342-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0 mM ivermectin). Additional mutations include C219A, C317S, C335S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C342-MTSL_1595% H2O/5% D2O
micelle160.2 mM [U-15N] S350C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 200 uM ivermectin, 0.4 % DMSO, 95% H2O/5% D2O15N-labeled, single-cysteine S350C-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0.2 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_S350C-MTSL_1695% H2O/5% D2O
micelle170.2 mM [U-15N] S350C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine S350C-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_S350C-MTSL_1795% H2O/5% D2O
micelle180.2 mM [U-15N] C375-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 200 uM ivermectin, 0.4 % DMSO, 95% H2O/5% D2O15N-labeled, single-cysteine C375-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0.2 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C385S, C390S, C427S, C435S, C443S, C449A, C460A. 15N-labeled, single-cysteine S350C-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0.2 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C375-MTSL_1895% H2O/5% D2O
micelle190.2 mM [U-15N] C375-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C375-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C385S, C390S, C427S, C435S, C443S, C449A, C460A. 15N-labeled, single-cysteine S350C-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0.2 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C375-MTSL_1995% H2O/5% D2O
micelle200.25 mM [U-15N] C390-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 250 uM ivermectin, 0.4 % DMSO, 95% H2O/5% D2O15N-labeled, single-cysteine C390-MTSL-labeled alpha7 TMD+ICD with 0- and 2.5-mM ascorbic acid for PRE NMR (0.25 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C427S, C435S, C443S, C449A, C460A.15N_a7_C390-MTSL_2095% H2O/5% D2O
micelle210.25 mM [U-15N] C390-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C390-MTSL-labeled alpha7 TMD+ICD with 0- and 2.5-mM ascorbic acid for PRE NMR (0 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C427S, C435S, C443S, C449A, C460A.15N_a7_C390-MTSL_2195% H2O/5% D2O
micelle220.24 mM [U-15N] L415C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 240 uM ivermectin, 0.4 % DMSO, 95% H2O/5% D2O15N-labeled, single-cysteine L415C-MTSL-labeled alpha7 TMD+ICD with 0- and 2.4-mM ascorbic acid for PRE NMR (0.24 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_L415C-MTSL_2295% H2O/5% D2O
micelle230.24 mM [U-15N] L415C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 35 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine L415C-MTSL-labeled alpha7 TMD+ICD with 0- and 2.4-mM ascorbic acid for PRE NMR (0 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_L415C-MTSL_2395% H2O/5% D2O
micelle240.2 mM [U-15N] C435-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 22 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 200 uM ivermectin, 0.4 % DMSO, 95% H2O/5% D2O15N-labeled, single-cysteine C435-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0.2 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C443S, C449A, C460A.15N_a7_C435-MTSL_2495% H2O/5% D2O
micelle250.2 mM [U-15N] C435-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 22 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C435-MTSL-labeled alpha7 TMD+ICD with 0- and 2.0-mM ascorbic acid for PRE NMR (0 mM ivermectin). Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C443S, C449A, C460A.15N_a7_C435-MTSL_2595% H2O/5% D2O
micelle260.22 mM [U-13C; U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 30 uM ivermectin, 30 uM PNU, 0.2 % DMSO, 95% H2O/5% D2O15N-, 13C-labeled single-cysteine C317 alpha7 TMD+ICD (30 uM ivermectin and 30 uM PNU). Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_13C_a7_C317_2695% H2O/5% D2O
micelle270.22 mM [U-13C; U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM sodium chloride, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled single-cysteine C317 alpha7 TMD+ICD (30 uM ivermectin and 30 uM PNU). Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_13C_a7_C317_2795% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMalpha7nAChR C317 TMD+ICD[U-15N]1
5 mMsodium acetatenatural abundance1
35 mMLDAOnatural abundance1
25 mMsodium chloridenatural abundance1
5 %D2Onatural abundance1
20 uMDSSnatural abundance1
0.25 mMalpha7nAChR C317 TMD+ICD[U-15N]2
5 mMsodium acetatenatural abundance2
35 mMLDAOnatural abundance2
25 mMsodium chloridenatural abundance2
5 %D2Onatural abundance2
20 uMDSSnatural abundance2
30 uMivermectinnatural abundance2
0.1 %DMSOnatural abundance2
0.25 mMalpha7nAChR C317 TMD+ICD[U-15N]3
5 mMsodium acetatenatural abundance3
35 mMLDAOnatural abundance3
25 mMsodium chloridenatural abundance3
5 %D2Onatural abundance3
20 uMDSSnatural abundance3
100 uMivermectinnatural abundance3
0.3 %DMSOnatural abundance3
0.25 mMalpha7nAChR C317 TMD+ICD[U-15N]4
5 mMsodium acetatenatural abundance4
35 mMLDAOnatural abundance4
25 mMsodium chloridenatural abundance4
5 %D2Onatural abundance4
20 uMDSSnatural abundance4
250 uMivermectinnatural abundance4
0.55 %DMSOnatural abundance4
0.25 mMalpha7nAChR C317 TMD+ICD[U-15N]5
5 mMsodium acetatenatural abundance5
35 mMLDAOnatural abundance5
25 mMsodium chloridenatural abundance5
5 %D2Onatural abundance5
20 uMDSSnatural abundance5
500 uMivermectinnatural abundance5
0.95 %DMSOnatural abundance5
0.25 mMalpha7nAChR C317 TMD+ICD[U-15N]6
5 mMsodium acetatenatural abundance6
35 mMLDAOnatural abundance6
25 mMsodium chloridenatural abundance6
5 %D2Onatural abundance6
20 uMDSSnatural abundance6
500 uMivermectinnatural abundance6
0.8 %DMSOnatural abundance6
0.25 mMalpha7nAChR C317 TMD+ICD[U-15N]7
5 mMsodium acetatenatural abundance7
35 mMLDAOnatural abundance7
25 mMsodium chloridenatural abundance7
5 %D2Onatural abundance7
20 uMDSSnatural abundance7
500 uMivermectinnatural abundance7
0.8 %DMSOnatural abundance7
0.25 mMalpha7nAChR C317 TMD+ICD[U-15N]8
5 mMsodium acetatenatural abundance8
35 mMLDAOnatural abundance8
25 mMsodium chloridenatural abundance8
5 %D2Onatural abundance8
20 uMDSSnatural abundance8
500 uMivermectinnatural abundance8
0.8 %DMSOnatural abundance8
0.20 mMalpha7nAChR C317 TMD+ICD[U-15N]9
5 mMsodium acetatenatural abundance9
35 mMLDAOnatural abundance9
25 mMsodium chloridenatural abundance9
5 %D2Onatural abundance9
20 uMDSSnatural abundance9
500 uMivermectinnatural abundance9
0.8 %DMSOnatural abundance9
0.22 mMV311C-MTSL alpha7nAChR TMD+ICD[U-15N]10
5 mMsodium acetatenatural abundance10
35 mMLDAOnatural abundance10
25 mMsodium chloridenatural abundance10
5 %D2Onatural abundance10
20 uMDSSnatural abundance10
220 uMivermectinnatural abundance10
0.4 %DMSOnatural abundance10
0.22 mMV311C-MTSL alpha7nAChR TMD+ICD[U-15N]11
5 mMsodium acetatenatural abundance11
35 mMLDAOnatural abundance11
25 mMsodium chloridenatural abundance11
5 %D2Onatural abundance11
20 uMDSSnatural abundance11
0.22 mMC335-MTSL alpha7nAChR TMD+ICD[U-15N]12
5 mMsodium acetatenatural abundance12
26 mMLDAOnatural abundance12
25 mMsodium chloridenatural abundance12
5 %D2Onatural abundance12
20 uMDSSnatural abundance12
220 uMivermectinnatural abundance12
0.4 %DMSOnatural abundance12
0.22 mMC335-MTSL alpha7nAChR TMD+ICD[U-15N]13
5 mMsodium acetatenatural abundance13
26 mMLDAOnatural abundance13
25 mMsodium chloridenatural abundance13
5 %D2Onatural abundance13
20 uMDSSnatural abundance13
0.2 mMC342-MTSL alpha7nAChR TMD+ICD[U-15N]14
5 mMsodium acetatenatural abundance14
26 mMLDAOnatural abundance14
25 mMsodium chloridenatural abundance14
5 %D2Onatural abundance14
20 uMDSSnatural abundance14
200 uMivermectinnatural abundance14
0.4 %DMSOnatural abundance14
0.2 %C342-MTSL alpha7nAChR TMD+ICD[U-15N]15
5 mMsodium acetatenatural abundance15
26 mMLDAOnatural abundance15
25 mMsodium chloridenatural abundance15
5 %D2Onatural abundance15
20 uMDSSnatural abundance15
0.2 mMS350C-MTSL alpha7nAChR TMD+ICD[U-15N]16
5 mMsodium acetatenatural abundance16
44 mMLDAOnatural abundance16
25 mMsodium chloridenatural abundance16
5 %D2Onatural abundance16
20 uMDSSnatural abundance16
200 uMivermectinnatural abundance16
0.4 %DMSOnatural abundance16
0.2 mMS350C-MTSL alpha7nAChR TMD+ICD[U-15N]17
5 mMsodium acetatenatural abundance17
44 mMLDAOnatural abundance17
25 mMsodium chloridenatural abundance17
5 %D2Onatural abundance17
20 uMDSSnatural abundance17
0.2 mMC375-MTSL alpha7nAChR TMD+ICD[U-15N]18
5 mMsodium acetatenatural abundance18
35 mMLDAOnatural abundance18
25 mMsodium chloridenatural abundance18
5 %D2Onatural abundance18
20 uMDSSnatural abundance18
200 uMivermectinnatural abundance18
0.4 %DMSOnatural abundance18
0.2 mMC375-MTSL alpha7nAChR TMD+ICD[U-15N]19
5 mMsodium acetatenatural abundance19
35 mMLDAOnatural abundance19
25 mMsodium chloridenatural abundance19
5 %D2Onatural abundance19
20 uMDSSnatural abundance19
0.25 mMC390-MTSL alpha7nAChR TMD+ICD[U-15N]20
5 mMsodium acetatenatural abundance20
44 mMLDAOnatural abundance20
25 mMsodium chloridenatural abundance20
5 %D2Onatural abundance20
20 uMDSSnatural abundance20
250 uMivermectinnatural abundance20
0.4 %DMSOnatural abundance20
0.25 mMC390-MTSL alpha7nAChR TMD+ICD[U-15N]21
5 mMsodium acetatenatural abundance21
44 mMLDAOnatural abundance21
25 mMsodium chloridenatural abundance21
5 %D2Onatural abundance21
20 uMDSSnatural abundance21
0.24 mML415C-MTSL alpha7nAChR TMD+ICD[U-15N]22
5 mMsodium acetatenatural abundance22
35 mMLDAOnatural abundance22
25 mMsodium chloridenatural abundance22
5 %D2Onatural abundance22
20 uMDSSnatural abundance22
240 uMivermectinnatural abundance22
0.4 %DMSOnatural abundance22
0.24 mML415C-MTSL alpha7nAChR TMD+ICD[U-15N]23
5 mMsodium acetatenatural abundance23
35 mMLDAOnatural abundance23
25 mMsodium chloridenatural abundance23
5 %D2Onatural abundance23
20 uMDSSnatural abundance23
0.2 mMC435-MTSL alpha7nAChR TMD+ICD[U-15N]24
5 mMsodium acetatenatural abundance24
22 mMLDAOnatural abundance24
25 mMsodium chloridenatural abundance24
5 %D2Onatural abundance24
20 uMDSSnatural abundance24
200 uMivermectinnatural abundance24
0.4 %DMSOnatural abundance24
0.2 mMC435-MTSL alpha7nAChR TMD+ICD[U-15N]25
5 mMsodium acetatenatural abundance25
22 mMLDAOnatural abundance25
25 mMsodium chloridenatural abundance25
5 %D2Onatural abundance25
20 uMDSSnatural abundance25
0.22 mMalpha7nAChR C317 TMD+ICD[U-13C; U-15N]26
5 mMsodium acetatenatural abundance26
44 mMLDAOnatural abundance26
25 mMsodium chloridenatural abundance26
5 %D2Onatural abundance26
20 uMDSSnatural abundance26
30 uMivermectinnatural abundance26
30 uMPNUnatural abundance26
0.2 %DMSOnatural abundance26
0.22 mMalpha7nAChR C317 TMD+ICD[U-13C; U-15N]27
5 mMsodium acetatenatural abundance27
44 mMLDAOnatural abundance27
25 mMsodium chloridenatural abundance27
5 %D2Onatural abundance27
20 uMDSSnatural abundance27
Sample conditionsIonic strength: 25 mM / Label: condition_s1 / pH: 4.7 / Pressure: 1 atm / Temperature: 318 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
NMRPipe10.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.19Goddarddata analysis
NMRFAM-SPARKY1.47Lee, Tonelli and Markleydata analysis
CS-ROSETTA3.17Shen, Vernon, Baker and Baxstructure calculation
Rosetta3.7Leaver-Fay, Tyka, Lewis, Lange, Thompson, Jacak, Kaufman, Renfrew, Smith, Sheffler, Davis, Cooper, Treuille, Mandell, Richter, Ban, Fleishman, Corn, Kim, Lyskov, Berrondo, Mentzer, Popovic, Havranek, Karanicolas, Das, Meiler, Kortemme, Gray, Kuhlman, Baker, and Bradleystructure calculation
Rosetta3.7Leaver-Fay, Tyka, Lewis, Lange, Thompson, Jacak, Kaufman, Renfrew, Smith, Sheffler, Davis, Cooper, Treuille, Mandell, Richter, Ban, Fleishman, Corn, Kim, Lyskov, Berrondo, Mentzer, Popovic, Havranek, Karanicolas, Das, Meiler, Kortemme, Gray, Kuhlman, Baker, and Bradleyrefinement
MolProbityRichardsonrefinement
Refinement
MethodSoftware ordinal
na7
na8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 15

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