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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
8TFD
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BU of 8tfd by Molmil
Crystal structure of a stem-loop DNA aptamer complexed with SARS-CoV-2 nucleocapsid protein RNA-binding domain
分子名称: 1,2-ETHANEDIOL, DNA aptamer, Nucleoprotein
著者Esler, M, Belica, C, Shi, K, Aihara, H.
登録日2023-07-10
公開日2024-11-13
最終更新日2024-12-11
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain.
Nucleic Acids Res., 52, 2024
8WUR
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BU of 8wur by Molmil
Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with shikonin
分子名称: 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione, 3C-like proteinase nsp5
著者Zhao, Z.Y, Li, W.W, Zhang, J, Li, J.
登録日2023-10-21
公開日2024-11-13
実験手法X-RAY DIFFRACTION (2.08 Å)
主引用文献Structural Basis for the Inhibition of SARS-CoV-2 M pro D48N Mutant by Shikonin and PF-07321332.
Viruses, 16, 2023
8WYH
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BU of 8wyh by Molmil
The global map of Omicron Subvariants Spike with ACE2
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Yan, R.H, Wang, A.J, Yang, H.N.
登録日2023-10-31
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献The global map of Omicron Subvariants Spike with ACE2
To Be Published
8WYJ
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BU of 8wyj by Molmil
The global map of Omicron Subvariants Spike with two antibodies
分子名称: S309-HC, S309-KC, SA55-HC, ...
著者Yan, R.H, Wang, A.J, Yang, H.N.
登録日2023-10-31
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献The global map of Omicron Subvariants Spike with two antibodies
To Be Published
8XZ8
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BU of 8xz8 by Molmil
BA.2.86 Spike in complex with bovine ACE2 (bound 1 ACE2)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
著者Yue, C, Liu, P.
登録日2024-01-21
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.65 Å)
主引用文献BA.2.86 Spike in complex with bovine ACE2
To Be Published
8XZ9
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BU of 8xz9 by Molmil
BA.2.86 Spike in complex with bovine ACE2 (bound 2 ACE2)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Yue, C, Liu, P.
登録日2024-01-21
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.37 Å)
主引用文献BA.2.86 Spike in complex with bovine ACE2
To Be Published
8XZA
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BA.2.86 Spike in complex with bovine ACE2 (Local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
著者Yue, C, Liu, P.
登録日2024-01-21
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (4.07 Å)
主引用文献BA.2.86 Spike in complex with bovine ACE2
To Be Published
8Y32
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BA.2.86-V483 RBD in complex with bACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
著者Yue, C, Liu, P.
登録日2024-01-28
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (4.13 Å)
主引用文献BA.2.86-V483 RBD in complex with bACE2
To Be Published
9F2G
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BU of 9f2g by Molmil
Crystal structure of SARS-CoV-2 N-protein C-terminal domain (apo form)
分子名称: GLYCEROL, Nucleoprotein, SULFATE ION
著者Marquez-Monino, M.A, Gonzalez, B, Perez-Canadillas, J.M.
登録日2024-04-23
公開日2024-11-13
最終更新日2025-01-15
実験手法X-RAY DIFFRACTION (1.57 Å)
主引用文献The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.
Structure, 33, 2025
9F2H
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Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole
分子名称: 1,2-ETHANEDIOL, 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine, Nucleoprotein, ...
著者Marquez-Monino, M.A, Gonzalez, B, Perez-Canadillas, J.M.
登録日2024-04-23
公開日2024-11-13
最終更新日2025-01-15
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.
Structure, 33, 2025
9F2I
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BU of 9f2i by Molmil
Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with 2-amino-1,3-benzothiazol-6-ol
分子名称: 1,2-ETHANEDIOL, 2-amino-1,3-benzothiazol-6-ol, Nucleoprotein, ...
著者Marquez-Monino, M.A, Gonzalez, B, Perez-Canadillas, J.M.
登録日2024-04-23
公開日2024-11-13
最終更新日2025-01-15
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.
Structure, 33, 2025
8W1T
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BU of 8w1t by Molmil
SARS-CoV-2 Main protease bound to a non-covalent non-peptidic HTS hit
分子名称: (5-bromopyridin-3-yl){4-[(R)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}methanone, (5-bromopyridin-3-yl){4-[(S)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}methanone, 1,2-ETHANEDIOL, ...
著者Bian, X, Tang, S, Sacchettini, J.C.
登録日2024-02-18
公開日2024-11-20
実験手法X-RAY DIFFRACTION (1.76 Å)
主引用文献An oral non-covalent non-peptidic inhibitor of SARS-CoV-2 Mpro ameliorates viral replication and pathogenesis in vivo.
Cell Rep, 43, 2024
8W1U
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SARS-CoV-2 Main protease bound to non-covalent lead molecule NZ-804
分子名称: 11-[1-(1H-pyrrolo[3,2-c]pyridine-7-carbonyl)piperidin-4-ylidene]-6,11-dihydro-5H-5lambda~6~-dibenzo[b,e]thiepine-5,5-dione, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
著者Bian, X, Tang, S, Sacchettini, J.C.
登録日2024-02-18
公開日2024-11-20
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献An oral non-covalent non-peptidic inhibitor of SARS-CoV-2 Mpro ameliorates viral replication and pathogenesis in vivo.
Cell Rep, 43, 2024
9C44
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SARS-CoV-2 S + S2L20
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, S2L20 Fab Heavy Chain Variable, ...
著者McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2024-06-03
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Design of customized coronavirus receptors.
Nature, 635, 2024
9C45
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BU of 9c45 by Molmil
SARS-CoV-2 S + S2L20 (local refinement of NTD and S2L20 Fab variable region)
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, S2L20 Fab Heavy Chain Variable, ...
著者McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2024-06-03
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Design of customized coronavirus receptors.
Nature, 635, 2024
9CO6
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BA.5 spike/Nanosota-9 complex
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, Nanosota-9, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-07-16
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (3.01 Å)
主引用文献Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO7
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Local refinement of BA.5 spike/Nanosota-9 complex
分子名称: Nanosota-9, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-07-16
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (3.32 Å)
主引用文献Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO8
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BU of 9co8 by Molmil
JN.1 spike/Nanosota-9 complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-9, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-07-16
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (2.99 Å)
主引用文献Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO9
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BU of 9co9 by Molmil
Local refinement of JN.1 spike/Nanosota-9 complex
分子名称: Nanosota-9, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-07-16
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9EVY
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BU of 9evy by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant E136D
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-04-02
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9EWH
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BU of 9ewh by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Y109A
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-04-03
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.93 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9EXB
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BU of 9exb by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain NTD
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-04-06
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9EZB
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BU of 9ezb by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P67S
分子名称: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-04-11
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F5J
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BU of 9f5j by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Q58I
分子名称: CADMIUM ION, Nucleoprotein
著者Dhamotharan, K, Schlundt, A.
登録日2024-04-29
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F5L
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BU of 9f5l by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant A119S
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A.
登録日2024-04-29
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2.363 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024

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件を2025-05-28に公開中

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