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

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基本情報

登録情報
データベース: PDB / ID: 8f4v
タイトルAlpha7 nicotinic acetylcholine receptor intracellular and transmembrane domains bound to ivermectin in a desensitized state
要素Neuronal acetylcholine receptor subunit alpha-7
キーワードMEMBRANE PROTEIN / nicotinic acetylcholine receptor / transmembrane and intracellular domain / desensitized state / ivermectin
機能・相同性
機能・相同性情報


sensory processing / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity ...sensory processing / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / plasma membrane raft / modulation of excitatory postsynaptic potential / response to amyloid-beta / positive regulation of excitatory postsynaptic potential / negative regulation of tumor necrosis factor production / monoatomic ion channel activity / toxic substance binding / monoatomic ion transport / positive regulation of protein metabolic process / positive regulation of long-term synaptic potentiation / response to nicotine / synapse organization / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / amyloid-beta binding / monoatomic ion transmembrane transport / postsynaptic membrane / postsynapse / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / learning or memory / response to hypoxia / neuron projection / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / synapse / signal transduction / protein homodimerization activity / membrane / plasma membrane
類似検索 - 分子機能
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
類似検索 - ドメイン・相同性
Chem-IVM / Neuronal acetylcholine receptor subunit alpha-7
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法溶液NMR / na
データ登録者Bondarenko, V. / Chen, Q. / Tang, P.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA046939 米国
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)T32GM075770 米国
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)T32EB009403 米国
引用ジャーナル: Acs Chem Neurosci / 年: 2023
タイトル: Structural Elucidation of Ivermectin Binding to alpha 7nAChR and the Induced Channel Desensitization.
著者: Bondarenko, V. / Chen, Q. / Singewald, K. / Haloi, N. / Tillman, T.S. / Howard, R.J. / Lindahl, E. / Xu, Y. / Tang, P.
履歴
登録2022年11月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年2月22日Provider: repository / タイプ: Initial release
改定 1.12023年3月8日Group: Database references / カテゴリ: 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
改定 1.22023年3月29日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年5月15日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)153,53410
ポリマ－149,1595
非ポリマー4,3755
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: NMR Distance Restraints
タイプ名称対称操作数
identity operation1_5551
Buried area21370 Å2
ΔGint-157 kcal/mol
Surface area80780 Å2
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)15 / 1000structures with the lowest energy
代表モデルモデル #1lowest energy

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要素

#1: タンパク質
Neuronal acetylcholine receptor subunit alpha-7


分子量: 29831.779 Da / 分子数: 5
断片: Transmembrane domain and intracellular domain residues 231-496
変異: A263S, V268S, L270S, A474E / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CHRNA7, NACHRA7 / プラスミド: pTBSG1-TMD+ICD / Cell (発現宿主): E. coli / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Rosetta 2(DE3) pLysS / 参照: UniProt: P36544
#2: 化合物
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


分子量: 875.093 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C48H74O14 / タイプ: SUBJECT OF INVESTIGATION / コメント: 抗寄生虫剤*YM
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: 溶液NMR
NMR実験
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDタイプ
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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試料調製

詳細
タイプSolution-ID内容詳細Label溶媒系
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
試料
濃度 (mg/ml)構成要素Isotopic 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
試料状態イオン強度: 25 mM / Label: condition_s1 / pH: 4.7 / 圧: 1 atm / 温度: 318 K

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NMR測定

NMRスペクトロメータータイプ: Bruker AVANCE II / 製造業者: Bruker / モデル: AVANCE II / 磁場強度: 800 MHz

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解析

NMR software
名称バージョン開発者分類
TopSpin3.2Bruker Biospincollection
NMRPipe10.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax解析
Sparky3.19Goddardデータ解析
NMRFAM-SPARKY1.47Lee, Tonelli and Markleyデータ解析
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 Bradley精密化
MolProbityRichardson精密化
精密化
手法ソフトェア番号
na7
na8
代表構造選択基準: lowest energy
NMRアンサンブルコンフォーマー選択の基準: structures with the lowest energy
計算したコンフォーマーの数: 1000 / 登録したコンフォーマーの数: 15

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る