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新型コロナウイルスの構造情報

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コロナウイルス
コロナウイルス, 2020. David S. Goodsell@RCSB PDB による原画を修正

最近、新型コロナウイルス感染症(Novel Coronavirus disease 2019: COVID-19)の拡大が世界中で深刻な問題となっています。早急にこの新型ウイルス(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)を理解し有効な薬を開発するため,関連するタンパク質の構造研究は既に始まっています。そして,解明された構造はPDBに登録されていっています。PDBjでは利用者の利便を図るため,新型コロナウイルス特集ページを作成しました。新たなエントリーが毎週水曜日の週次更新で公開されると、同時にこのページにも追加されます。

またこのウイルスのタンパク質に関する解説記事を以下の「今月の分子」ページに掲載しています。

「全エントリー」のタブでは,同じ著者によるグループ登録のエントリーも全て区別し,すべてのPDB IDを省略せず表示しています。 「代表構造」タブには最も分解能の高い代表構造のみを表示しており,アミノ酸配列が100%同じPDBエントリーはリガンドが異なるものも含め除外してあります。 「最新のエントリー」のタブは,今週公開された最も新しいエントリーです。


作成日: 2020-09-03 (最終更新日: more than 1 year ago)2022-09-02
7DJR
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BU of 7djr by Molmil
Crystal structure of SARS-CoV-2 main protease (no ligand)
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE
著者Deetanya, P, Wangkanont, K.
登録日2020-11-21
公開日2021-06-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification.
Comput Struct Biotechnol J, 19, 2021
7EXM
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BU of 7exm by Molmil
The N-terminal crystal structure of SARS-CoV-2 NSP2
分子名称: GLYCEROL, Non-structural protein 2, ZINC ION
著者Ma, J, Chen, Z.
登録日2021-05-27
公開日2021-06-16
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (1.96 Å)
主引用文献Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2.
Virol Sin, 36, 2021
7MY2
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BU of 7my2 by Molmil
CryoEM structure of neutralizing nanobody Nb30 in complex with SARS-CoV2 spike
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody Nb30, ...
著者Xu, K, Kwong, P.D.
登録日2021-05-20
公開日2021-06-16
最終更新日2021-07-28
実験手法ELECTRON MICROSCOPY (2.65 Å)
主引用文献Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants.
Nature, 595, 2021
7MY3
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CryoEM structure of neutralizing nanobody Nb12 in complex with SARS-CoV2 spike
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody Nb12, ...
著者Xu, K, Kwong, P.D.
登録日2021-05-20
公開日2021-06-16
最終更新日2021-07-28
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants.
Nature, 595, 2021
7N5Z
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BU of 7n5z by Molmil
SARS-CoV-2 Main protease C145S mutant
分子名称: 3C-like proteinase
著者Noske, G.D, Nakamura, A.M, Gawriljuk, V.O, Lima, G.M.A, Zeri, A.C.M, Nascimento, A.F.Z, Oliva, G, Godoy, A.S.
登録日2021-06-07
公開日2021-06-16
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.76 Å)
主引用文献A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.
J.Mol.Biol., 433, 2021
7N6N
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SARS-CoV-2 Main protease C145S mutant in complex with N and C-terminal residues
分子名称: 3C-like proteinase
著者Noske, G.D, Nakamura, A.M, Gawriljuk, V.O, Lima, G.M.A, Zeri, A.C.M, Nascimento, A.F.Z, Fernandes, R.S, Oliva, G, Godoy, A.S.
登録日2021-06-08
公開日2021-06-16
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.
J.Mol.Biol., 433, 2021
7NT1
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Crystal structure of SARS CoV2 main protease in complex with FSP007
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE, [(2R)-1-[2-(1H-indol-3-yl)ethylamino]-1-oxidanylidene-butan-2-yl] prop-2-enoate
著者Oerlemans, R, Eris, D, Wang, M, Sharpe, M, Domling, A, Groves, M.R.
登録日2021-03-08
公開日2021-06-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.85 Å)
主引用文献Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.
Angew.Chem.Int.Ed.Engl., 60, 2021
7NT2
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Crystal structure of SARS CoV2 main protease in complex with FSP006
分子名称: 3C-like proteinase, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ...
著者Oerlemans, R, Eris, D, Wang, M, Sharpe, M, Domling, A, Groves, M.R.
登録日2021-03-08
公開日2021-06-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.145 Å)
主引用文献Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.
Angew.Chem.Int.Ed.Engl., 60, 2021
7NT3
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BU of 7nt3 by Molmil
Crystal structure of SARS CoV2 main protease in complex with FSCU015
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE, ~{N}-[(1~{S})-2-(1,3-benzodioxol-5-ylmethylamino)-1-(3-hydroxyphenyl)-2-oxidanylidene-ethyl]-~{N}-propyl-prop-2-enamide
著者Oerlemans, R, Eris, D, Wang, M, Sharpe, M, Domling, A, Groves, M.R.
登録日2021-03-08
公開日2021-06-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.325 Å)
主引用文献Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.
Angew.Chem.Int.Ed.Engl., 60, 2021
7NTK
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BU of 7ntk by Molmil
PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex
分子名称: 1,2-ETHANEDIOL, CITRATE ANION, Envelope small membrane protein, ...
著者Javorsky, A, Kvansakul, M.
登録日2021-03-10
公開日2021-06-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain.
Commun Biol, 4, 2021
7NTV
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BU of 7ntv by Molmil
Crystal structure of SARS CoV2 main protease in complex with DN_EG_002 (modelled using PanDDA event map)
分子名称: 2-acetamido-N-cyclopropyl-5-phenyl-thiophene-3-carboxamide, 3C-like proteinase, DIMETHYL SULFOXIDE
著者Oerlemans, R, Eris, D, Wang, M, Sharpe, M, Domling, A, Groves, M.R.
登録日2021-03-10
公開日2021-06-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.065 Å)
主引用文献Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.
Angew.Chem.Int.Ed.Engl., 60, 2021
7NUK
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BU of 7nuk by Molmil
Crystal structure of SARS CoV2 main protease in complex with EG009 (modelled using PanDDA event map)
分子名称: 2-[2-chloranylethanoyl(propyl)amino]-~{N}-(2-methoxyphenyl)ethanamide, 3C-like proteinase, DIMETHYL SULFOXIDE
著者Oerlemans, R, Eris, D, Wang, M, Sharpe, M, Domling, A, Groves, M.R.
登録日2021-03-12
公開日2021-06-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.19 Å)
主引用文献Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.
Angew.Chem.Int.Ed.Engl., 60, 2021
7CUT
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BU of 7cut by Molmil
Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with Z-VAD-FMK
分子名称: 3C protein, DIMETHYL SULFOXIDE, GLYCEROL, ...
著者Lu, M, Yang, H.T, Wang, Z.Y, Zhao, Y, Xing, Y.F.
登録日2020-08-24
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.82 Å)
主引用文献Identification of proteasome and caspase inhibitors targeting SARS-CoV-2 M pro .
Signal Transduct Target Ther, 6, 2021
7CUU
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BU of 7cuu by Molmil
Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with MG132
分子名称: 3C protein, DIMETHYL SULFOXIDE, GLYCEROL, ...
著者Lu, M, Yang, H.T, Wang, Z.Y, Zhao, Y, Xing, Y.F.
登録日2020-08-24
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.68 Å)
主引用文献Identification of proteasome and caspase inhibitors targeting SARS-CoV-2 M pro .
Signal Transduct Target Ther, 6, 2021
7CWT
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BU of 7cwt by Molmil
SARS-CoV-2 Spike protein in complex with hb27 and fc05 Fab cocktail
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain Fab of FC05, Heavy chain Fab of HB27, ...
著者Cui, Z, Wang, X.
登録日2020-08-31
公開日2021-06-23
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Structure-based development of human antibody cocktails against SARS-CoV-2.
Cell Res., 31, 2021
7E18
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BU of 7e18 by Molmil
Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53
分子名称: 1,2-ETHANEDIOL, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, Replicase polyprotein 1ab
著者Senda, M, Konno, S, Hayashi, Y, Senda, T.
登録日2021-02-01
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
J.Med.Chem., 65, 2022
7E19
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BU of 7e19 by Molmil
Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor SH-5
分子名称: (phenylmethyl) N-[(2S)-1-[[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate, 3C-like proteinase
著者Senda, M, Konno, S, Hayashi, Y, Senda, T.
登録日2021-02-01
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.15 Å)
主引用文献3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
J.Med.Chem., 65, 2022
7E5Y
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Molecular basis for neutralizing antibody 2B11 targeting SARS-CoV-2 RBD
分子名称: 2B11 Fab Heavy chain, 2B11 Fab Light chain, Spike protein S1
著者Wu, H, Yu, F, Wang, Q.S, Zhou, H, Wang, W.W, Zhao, T, Pan, Y.B, Yang, X.M.
登録日2021-02-21
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.59 Å)
主引用文献Screening of potent neutralizing antibodies against SARS-CoV-2 using convalescent patients-derived phage-display libraries.
Cell Discov, 7, 2021
7EAZ
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BU of 7eaz by Molmil
Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 1
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
登録日2021-03-08
公開日2021-06-23
最終更新日2022-01-05
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation.
J.Biol.Chem., 297, 2021
7EB0
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Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
登録日2021-03-08
公開日2021-06-23
最終更新日2022-01-05
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation.
J.Biol.Chem., 297, 2021
7EB3
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BU of 7eb3 by Molmil
Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 3
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
登録日2021-03-08
公開日2021-06-23
最終更新日2022-01-05
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation.
J.Biol.Chem., 297, 2021
7EB4
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BU of 7eb4 by Molmil
Cryo-EM structure of SARS-CoV-2 Spike D614G variant, two RBD-up conformation 1
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
登録日2021-03-08
公開日2021-06-23
最終更新日2022-01-05
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation.
J.Biol.Chem., 297, 2021
7EB5
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BU of 7eb5 by Molmil
Cryo-EM structure of SARS-CoV-2 Spike D614G variant, two RBD-up conformation 2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
登録日2021-03-08
公開日2021-06-23
最終更新日2022-01-05
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation.
J.Biol.Chem., 297, 2021
7EJ4
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Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-25
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RBD-chAb-25, ...
著者Yang, T.J, Yu, P.Y, Wu, H.C, Hsu, S.T.D.
登録日2021-04-01
公開日2021-06-23
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-25
To be published
7EJ5
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Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-45
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RBD-chAb45, ...
著者Yang, T.J, Yu, P.Y, Wu, H.C, Hsu, S.T.D.
登録日2021-04-01
公開日2021-06-23
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-45
To Be Published

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件を2024-07-10に公開中

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