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基本情報

登録情報
データベース: PDB / ID: 7rpm
タイトルStructures of the Intracellular Domain and Transmembrane Domain of the Human alpha7 Nicotinic Acetylcholine Receptors
要素Neuronal acetylcholine receptor subunit alpha-7
キーワードMEMBRANE PROTEIN / nAChRs / intracellular domains / ion channels / Cys-loop receptors / intrinsically disordered regions / intrinsically disordered proteins
機能・相同性
機能・相同性情報


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 / chloride channel regulator activity / acetylcholine binding / regulation of amyloid precursor protein catabolic process / acetylcholine-gated monoatomic cation-selective channel activity / 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 / 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 / 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 / synapse / positive regulation of cell population proliferation / 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
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, 4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 of General Medical Sciences (NIH/NIGMS)T32GM075770 米国
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)T32EB009403 米国
National Science Foundation (NSF, United States)1148698 米国
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Structures of highly flexible intracellular domain of human alpha 7 nicotinic acetylcholine receptor.
著者: Bondarenko, V. / Wells, M.M. / Chen, Q. / Tillman, T.S. / Singewald, K. / Lawless, M.J. / Caporoso, J. / Brandon, N. / Coleman, J.A. / Saxena, S. / Lindahl, E. / Xu, Y. / Tang, P.
履歴
登録2021年8月3日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年1月19日Provider: repository / タイプ: Initial release
改定 1.12022年2月16日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
改定 1.22022年9月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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

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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


分子量 (理論値)分子数
合計 (水以外)149,1595
ポリマ－149,1595
非ポリマー00
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 area22570 Å2
ΔGint-206 kcal/mol
Surface area81700 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

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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
111isotropic22D 1H-15N TROSY-HSQC
121isotropic23D BEST-HNCA
131isotropic23D BEST-HN(CO)CA
141isotropic23D TROSY-CBCA(CO)NH
151isotropic23D BEST-HNCO
262isotropic22D 1H-15N TROSY-HSQC
272isotropic23D TROSY-HNCA
282isotropic23D TROSY-HN(CO)CA
292isotropic33D TROSY-HN(CA)CB
2102isotropic33D TROSY-CBCA(CO)NH
2112isotropic33D TROSY-HNCO
3123isotropic32D 1H-13C HSQC
3133isotropic33D 13C-edited NOESY-HSQC
4144isotropic12D 1H-15N TROSY-HSQC
4154isotropic13D 15N-edited NOESY-TROSY-HSQC
5165isotropic12D 1H-15N TROSY-HSQC
6176isotropic22D 1H-15N TROSY-HSQC
7187isotropic22D 1H-15N TROSY-HSQC
8198isotropic12D 1H-15N TROSY-HSQC
9209isotropic12D 1H-15N TROSY-HSQC
102110isotropic12D 1H-15N TROSY-HSQC
112211isotropic22D 1H-15N TROSY-HSQC
122312isotropic22D 1H-15N TROSY-HSQC
132413isotropic22D 1H-15N TROSY-HSQC
142514isotropic12D 1H-15N TROSY-HSQC
152615isotropic22D 1H-15N TROSY-HSQC
162716isotropic22D 1H-15N TROSY-HSQC
172817isotropic12D 1H-15N TROSY-HSQC
182918isotropic22D 1H-15N TROSY-HSQC
193019isotropic12D 1H-15N TROSY-HSQC
203120isotropic12D 1H-15N TROSY-HSQC
213221isotropic12D 1H-15N IPAP
223322isotropic12D 1H-15N TROSY-HSQC
233423isotropic12D 1H-15N IPAP
243524isotropic12D 1H-15N TROSY-HSQC
253625isotropic12D 1H-15N IPAP
263726isotropic22D 1H-15N TROSY-HSQC
263826isotropic23D TROSY-HNCA
263926isotropic23D TROSY-HN(CO)CA
274016isotropic22D 1H-15N TROSY-HSQC
284118isotropic22D 1H-15N TROSY-HSQC
294217isotropic12D 1H-15N TROSY-HSQC
304319isotropic12D 1H-15N TROSY-HSQC
30441isotropic22D 1H-15N TROSY-HSQC
30451isotropic23D BEST-HNCA
30461isotropic23D BEST-HN(CO)CA
30471isotropic23D TROSY-CBCA(CO)NH
30481isotropic23D BEST-HNCO

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試料調製

詳細
タイプSolution-ID内容詳細Label溶媒系
micelle10.24 mM [U-13C; U-15N] alpha7nAChR TMD+ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled alpha7 TMD+ICD for backbone 1H, 15N, 13C chemical shift assignment.15N_13C_a795% H2O/5% D2O
micelle20.25 mM [U-13C; U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled single-cysteine C317 alpha7 TMD+ICD for backbone 1H, 15N, 13C chemical shift assignment. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_13C_a7_C317_195% H2O/5% D2O
micelle260.35 mM [U-13C; U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled single-cysteine C317 alpha7 TMD+ICD for backbone 1H, 15N, 13C chemical shift assignment. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_13C_a7_C317_295% H2O/5% D2O
micelle30.25 mM [U-13C; U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled single-cysteine C317 alpha7 TMD+ICD for 3D 13C-edited NOESY-HSQC. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_13C_a7_C317_395% H2O/5% D2O
micelle40.35 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for 3D 15N-edited NOESY-TROSY-HSQC. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C31795% H2O/5% D2O
micelle50.22 mM [U-15N] V311C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 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. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_V311C-MTSL95% H2O/5% D2O
micelle60.22 mM [U-15N] C317-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C317-MTSL-labeled alpha7 TMD+ICD with 0 and 2.2 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317-MTSL95% H2O/5% D2O
micelle70.3 mM [U-15N] C335-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C335-MTSL-labeled alpha7 TMD+ICD with 0 and 3.0 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C335-MTSL95% H2O/5% D2O
micelle80.3 mM [U-15N] C342-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C342-MTSL-labeled alpha7 TMD+ICD with 0 and 3.0 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C342-MTSL95% H2O/5% D2O
micelle90.3 mM [U-15N] S350C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine S350C-MTSL-labeled alpha7 TMD+ICD with 0 and 3.0 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_S350C-MTSL95% H2O/5% D2O
micelle100.25 mM [U-15N] S358C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine S358C-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_S358C-MTSL95% H2O/5% D2O
micelle110.25 mM [U-15N] C375-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 66 mM LDAO, 20 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C375-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C375-MTSL95% H2O/5% D2O
micelle120.22 mM [U-15N] C390-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C390-MTSL-labeled alpha7 TMD+ICD with 0 and 2.2 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C427S, C435S, C443S, C449A, C460A.15N_a7_C390-MTSL95% H2O/5% D2O
micelle130.25 mM [U-15N] L415C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine L415C-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_L415C-MTSL95% H2O/5% D2O
micelle140.25 mM [U-15N] C427-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C427-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427-MTSL95% H2O/5% D2O
micelle150.25 mM [U-15N] C435-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C435-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C443S, C449A, C460A.15N_a7_C435-MTSL95% H2O/5% D2O
micelle160.28 mM V311C-MTSL alpha7 TMD-ICD, 0.07 mM [U-15N] V311C alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O0.28 mM V311C-MTSL-labeled alpha7 TMD-ICD mixed with 0.07 mM 15N-labeled V311C alpha7 TMD-ICD with 0 and 2.5 mM ascorbic acid for intersubunit PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_V311-MTSL_inter95% H2O/5% D2O
micelle180.28 mM V311C alpha7 TMD-ICD, 0.07 mM [U-15N] V311C-MTSL alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O0.28 mM V311C alpha7 TMD-ICD mixed with 0.07 mM 15N-labeled, V311C-MTSL-labeled alpha7 TMD-ICD with 0 and 1.4 mM ascorbic acid for intrasubunit PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_V311-MTSL_intra95% H2O/5% D2O
micelle170.24 mM C427-MTSL alpha7 TMD-ICD, 0.06 mM [U-15N] C427 alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O0.24 mM C427-MTSL-labeled alpha7 TMD-ICD mixed with 0.06 mM 15N-labeled C427 alpha7 TMD-ICD with 0 and 2.4 mM ascorbic acid for intersubunit PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427-MTSL_inter95% H2O/5% D2O
micelle190.24 mM C427 alpha7 TMD-ICD, 0.06 mM [U-15N] C427-MTSL alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O0.24 mM C427 alpha7 TMD-ICD mixed with 0.06 mM 15N-labeled, C427-MTSL-labeled alpha7 TMD-ICD with 0 and 1.2 mM ascorbic acid for intrasubunit PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427-MTSL_intra95% H2O/5% D2O
micelle200.25 mM [U-15N] C427-EDTA-Lu3+ alpha7 TMD-ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C427-labeled with a diamagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Lu3+ alpha7 TMD-ICD. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427_RDC_Lu3+95% H2O/5% D2O
micelle210.2 mM [U-15N] C427-EDTA-Tm3+ alpha7 TMD-ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C427-labeled with a paramagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Tm3+ alpha7 TMD-ICD. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427_RDC_Tm3+95% H2O/5% D2O
micelle220.25 mM [U-15N] C317-EDTA-Lu3+ alpha7 TMD-ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C317-labeled with a diamagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Lu3+ alpha7 TMD-ICD. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_RDC_Lu3+95% H2O/5% D2O
micelle230.25 mM [U-15N] C317-EDTA-Tm3+ alpha7 TMD-ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C317-labeled with a paramagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Tm3+ alpha7 TMD-ICD. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_RDC_Tm3+95% H2O/5% D2O
micelle240.24 mM [U-15N] C219-EDTA-Lu3+ alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C219-labeled with a diamagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Lu3+ alpha7 TMD-ICD. Additional mutations include C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C219_RDC_Lu3+95% H2O/5% D2O
micelle250.22 mM [U-15N] C219-EDTA-Tm3+ alpha7 TMD-ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C219-labeled with a paramagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Tm3+ alpha7 TMD-ICD. Additional mutations include C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C219_RDC_Tm3+95% H2O/5% D2O
試料
濃度 (mg/ml)構成要素Isotopic labelingSolution-ID
0.24 mMalpha7nAChR TMD+ICD[U-13C; U-15N]1
5 mMsodium acetatenatural abundance1
66 mMLDAOnatural abundance1
25 mMNaClnatural abundance1
5 %D2Onatural abundance1
20 uMDSSnatural abundance1
0.25 mMalpha7nAChR C317 TMD+ICD[U-13C; U-15N]2
5 mMsodium acetatenatural abundance2
44 mMLDAOnatural abundance2
25 mMNaClnatural abundance2
5 %D2Onatural abundance2
20 uMDSSnatural abundance2
0.35 mMalpha7nAChR C317 TMD+ICD[U-13C; U-15N]26
5 mMsodium acetatenatural abundance26
44 mMLDAOnatural abundance26
25 mMNaClnatural abundance26
5 %D2Onatural abundance26
20 uMDSSnatural abundance26
0.25 mMalpha7nAChR C317 TMD+ICD[U-13C; U-15N]3
5 mMsodium acetatenatural abundance3
44 mMLDAOnatural abundance3
25 mMNaClnatural abundance3
5 %D2Onatural abundance3
20 uMDSSnatural abundance3
0.35 mMalpha7nAChR C317 TMD+ICD[U-15N]4
5 mMsodium acetatenatural abundance4
66 mMLDAOnatural abundance4
25 mMNaClnatural abundance4
5 %D2Onatural abundance4
20 uMDSSnatural abundance4
0.22 mMV311C-MTSL alpha7nAChR TMD+ICD[U-15N]5
5 mMsodium acetatenatural abundance5
44 mMLDAOnatural abundance5
25 mMNaClnatural abundance5
5 %D2Onatural abundance5
20 uMDSSnatural abundance5
0.22 mMC317-MTSL alpha7nAChR TMD+ICD[U-15N]6
5 mMsodium acetatenatural abundance6
44 mMLDAOnatural abundance6
25 mMNaClnatural abundance6
5 %D2Onatural abundance6
20 uMDSSnatural abundance6
0.3 mMC335-MTSL alpha7nAChR TMD+ICD[U-15N]7
5 mMsodium acetatenatural abundance7
53 mMLDAOnatural abundance7
25 mMNaClnatural abundance7
5 %D2Onatural abundance7
20 uMDSSnatural abundance7
0.3 mMC342-MTSL alpha7nAChR TMD+ICD[U-15N]8
5 mMsodium acetatenatural abundance8
66 mMLDAOnatural abundance8
25 mMNaClnatural abundance8
5 %D2Onatural abundance8
20 uMDSSnatural abundance8
0.3 mMS350C-MTSL alpha7nAChR TMD+ICD[U-15N]9
5 mMsodium acetatenatural abundance9
53 mMLDAOnatural abundance9
25 mMNaClnatural abundance9
5 %D2Onatural abundance9
20 uMDSSnatural abundance9
0.25 mMS358C-MTSL alpha7nAChR TMD+ICD[U-15N]10
5 mMsodium acetatenatural abundance10
44 mMLDAOnatural abundance10
25 mMNaClnatural abundance10
5 %D2Onatural abundance10
20 uMDSSnatural abundance10
0.25 mMC375-MTSL alpha7nAChR TMD+ICD[U-15N]11
5 mMsodium acetatenatural abundance11
66 mMLDAOnatural abundance11
20 mMNaClnatural abundance11
5 %D2Onatural abundance11
20 uMDSSnatural abundance11
0.22 mMC390-MTSL alpha7nAChR TMD+ICD[U-15N]12
5 mMsodium acetatenatural abundance12
53 mMLDAOnatural abundance12
25 mMNaClnatural abundance12
5 %D2Onatural abundance12
20 uMDSSnatural abundance12
0.25 mML415C-MTSL alpha7nAChR TMD+ICD[U-15N]13
5 mMsodium acetatenatural abundance13
44 mMLDAOnatural abundance13
25 mMNaClnatural abundance13
5 %D2Onatural abundance13
20 uMDSSnatural abundance13
0.25 mMC427-MTSL alpha7nAChR TMD+ICD[U-15N]14
5 mMsodium acetatenatural abundance14
44 mMLDAOnatural abundance14
25 mMNaClnatural abundance14
5 %D2Onatural abundance14
20 uMDSSnatural abundance14
0.25 mMC435-MTSL alpha7nAChR TMD+ICD[U-15N]15
5 mMsodium acetatenatural abundance15
44 mMLDAOnatural abundance15
25 mMNaClnatural abundance15
5 %D2Onatural abundance15
20 uMDSSnatural abundance15
0.28 mMV311C-MTSL alpha7 TMD-ICDnatural abundance16
0.07 mMV311C alpha7 TMD-ICD[U-15N]16
5 mMsodium acetatenatural abundance16
44 mMLDAOnatural abundance16
25 mMNaClnatural abundance16
5 %D2Onatural abundance16
20 uMDSSnatural abundance16
0.28 mMV311C alpha7 TMD-ICDnatural abundance18
0.07 mMV311C-MTSL alpha7 TMD-ICD[U-15N]18
5 mMsodium acetatenatural abundance18
44 mMLDAOnatural abundance18
25 mMNaClnatural abundance18
5 %D2Onatural abundance18
20 uMDSSnatural abundance18
0.24 mMC427-MTSL alpha7 TMD-ICDnatural abundance17
0.06 mMC427 alpha7 TMD-ICD[U-15N]17
5 mMsodium acetatenatural abundance17
44 mMLDAOnatural abundance17
25 mMNaClnatural abundance17
5 %D2Onatural abundance17
20 uMDSSnatural abundance17
0.24 mMC427 alpha7 TMD-ICDnatural abundance19
0.06 mMC427-MTSL alpha7 TMD-ICD[U-15N]19
5 mMsodium acetatenatural abundance19
44 mMLDAOnatural abundance19
25 mMNaClnatural abundance19
5 %D2Onatural abundance19
20 uMDSSnatural abundance19
0.25 mMC427-EDTA-Lu3+ alpha7 TMD-ICD[U-15N]20
5 mMsodium acetatenatural abundance20
53 mMLDAOnatural abundance20
25 mMNaClnatural abundance20
5 %D2Onatural abundance20
20 uMDSSnatural abundance20
0.2 mMC427-EDTA-Tm3+ alpha7 TMD-ICD[U-15N]21
5 mMsodium acetatenatural abundance21
66 mMLDAOnatural abundance21
25 mMNaClnatural abundance21
5 %D2Onatural abundance21
20 uMDSSnatural abundance21
0.25 mMC317-EDTA-Lu3+ alpha7 TMD-ICD[U-15N]22
5 mMsodium acetatenatural abundance22
66 mMLDAOnatural abundance22
25 mMNaClnatural abundance22
5 %D2Onatural abundance22
20 uMDSSnatural abundance22
0.25 mMC317-EDTA-Tm3+ alpha7 TMD-ICD[U-15N]23
5 mMsodium acetatenatural abundance23
53 mMLDAOnatural abundance23
25 mMNaClnatural abundance23
5 %D2Onatural abundance23
20 uMDSSnatural abundance23
0.24 mMC219-EDTA-Lu3+ alpha7 TMD-ICD[U-15N]24
5 mMsodium acetatenatural abundance24
44 mMLDAOnatural abundance24
25 mMNaClnatural abundance24
5 %D2Onatural abundance24
20 uMDSSnatural abundance24
0.22 mMC219-EDTA-Tm3+ alpha7 TMD-ICD[U-15N]25
5 mMsodium acetatenatural abundance25
53 mMLDAOnatural abundance25
25 mMNaClnatural abundance25
5 %D2Onatural abundance25
20 uMDSSnatural abundance25
試料状態
Conditions-IDイオン強度LabelpH圧 (kPa)温度 (K)
125 mMcondition_s14.71 atm318 K
225 mMcondition_s24.71 atm318 K
2625 mMcondition_s264.71 atm318 K
325 mMcondition_s34.71 atm318 K
425 mMcondition_s44.71 atm318 K
525 mMcondition_s54.71 atm318 K
625 mMcondition_s64.71 atm318 K
725 mMcondition_s74.71 atm318 K
825 mMcondition_s84.71 atm318 K
925 mMcondition_s94.71 atm318 K
1025 mMcondition_s104.71 atm318 K
1125 mMcondition_s114.71 atm318 K
1225 mMcondition_s124.71 atm318 K
1325 mMcondition_s134.71 atm318 K
1425 mMcondition_s144.71 atm318 K
1525 mMcondition_s154.71 atm318 K
1625 mMcondition_s164.71 atm318 K
2725 mMcondition_s274.71 atm298 K
1825 mMcondition_s184.71 atm318 K
2825 mMcondition_s284.71 atm298 K
1725 mMcondition_s174.71 atm318 K
2925 mMcondition_s294.71 atm298 K
1925 mMcondition_s194.71 atm318 K
3025 mMcondition_s304.71 atm298 K
2025 mMcondition_s204.71 atm308 K
2125 mMcondition_s214.71 atm308 K
2225 mMcondition_s224.71 atm308 K
2325 mMcondition_s234.71 atm308 K
2425 mMcondition_s244.71 atm308 K
2525 mMcondition_s254.71 atm308 K

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NMR測定

NMRスペクトロメーター
タイプ製造業者モデル磁場強度 (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II9001
Bruker AVANCE IIBrukerAVANCE II8002
Bruker AVANCEBrukerAVANCE7003

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解析

NMR software
名称バージョン開発者分類
TopSpin2.1 and 3.1Bruker 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
PHENIX1.19Liebschner, Afonine, Baker, Bunkoczi, Chen, Croll, Hintze, Hung, Jain, McCoy, Moriarty, Oeffner, Poon, Prisant, Read, Richardson, Richardson, Sammito, Sobolev, Stockwell, Terwilliger, Urzhumtsev, Videau, Williams and Adams精密化
MolProbityRichardsonデータ解析
精密化
手法ソフトェア番号
na8
na9
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

-
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://pdbjlc1.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