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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
8Q7S
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BU of 8q7s by Molmil
Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01
分子名称: 1,2-ETHANEDIOL, 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE, GLYCEROL, ...
著者Guttler, T, Aksu, M, Gorlich, D.
登録日2023-08-16
公開日2023-12-20
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q93
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BU of 8q93 by Molmil
Crystal structure of the SARS-COV-2 RBD with neutralizing-VHHs Re30H02 and Re21D01
分子名称: Nanobody Re21D01, Nanobody Re30H02, Spike protein S1
著者Aksu, M, Guttler, T, Rymarenko, O, Gorlich, D.
登録日2023-08-19
公開日2023-12-20
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (3.1 Å)
主引用文献Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q94
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Crystal structure of The SARS-COV-2 BA.2.75 RBD with neutralizing-VHHs Re32D03 and Ma3B12
分子名称: Nanobody Ma3B12, Nanobody Re32D03, Spike protein S1
著者Aksu, M, Guttler, T, Gorlich, D.
登録日2023-08-19
公開日2023-12-20
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q95
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Crystal structure of the SARS-CoV-2 BA.1 RBD with neutralizing-VHHs Ma16B06 and Ma3F05
分子名称: Nanobody Ma16B06, Nanobody Ma3F05, Spike protein S1
著者Aksu, M, Rymarenko, O, Guttler, T, Gorlich, D.
登録日2023-08-19
公開日2023-12-20
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8XAB
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BU of 8xab by Molmil
Crystal structure of Ubl1 domain of nonstructural protein 3 of SARS-CoV-2
分子名称: GLYCEROL, Papain-like protease nsp3
著者Li, Y, Ke, Z.
登録日2023-12-03
公開日2023-12-20
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (1.49 Å)
主引用文献N terminus of SARS-CoV-2 nonstructural protein 3 interrupts RNA-driven phase separation of N protein by displacing RNA.
J.Biol.Chem., 300, 2024
7Y3O
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BU of 7y3o by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody BIOLS56
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of BIOLS56, Light chain of BIOLS56, ...
著者Rao, X, Gao, F, Wu, Y, Gao, F.
登録日2022-06-11
公開日2023-12-27
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
8BZN
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BU of 8bzn by Molmil
SARS-CoV-2 non-structural protein 10 (nsp10) variant T102I
分子名称: CHLORIDE ION, DIMETHYL SULFOXIDE, Replicase polyprotein 1ab, ...
著者Wang, H, Rizvi, S.R.A, Dong, D, Lou, J, Wang, Q, Sopipong, W, Najar, F, Agarwal, P.K, Kozielski, F, Haider, S.
登録日2022-12-15
公開日2023-12-27
最終更新日2024-01-10
実験手法X-RAY DIFFRACTION (2.19 Å)
主引用文献Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16.
Elife, 12, 2023
8HN4
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Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope QYIKWPWYI
分子名称: Beta-2-microglobulin, MHC class I antigen, SARS-CoV-2 T-cell epitope QYIKWPWYI
著者Deng, S.S, Jin, T.C, Xu, Z.H.
登録日2022-12-07
公開日2023-12-27
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.853 Å)
主引用文献Immune escape at SARS- CoV-2 killer T cell epitope
To be published
8HVK
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BU of 8hvk by Molmil
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with PF07321332
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Zeng, P, Zhang, J, Li, J.
登録日2022-12-27
公開日2023-12-27
最終更新日2025-07-09
実験手法X-RAY DIFFRACTION (1.63 Å)
主引用文献Evaluation of the Inhibition Potency of Nirmatrelvir against Main Protease Mutants of SARS-CoV-2 Variants.
Biochemistry, 62, 2023
8HVL
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BU of 8hvl by Molmil
Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with PF07321332
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Zou, X.F, Zhang, J, Li, J.
登録日2022-12-27
公開日2023-12-27
最終更新日2025-07-09
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Evaluation of the Inhibition Potency of Nirmatrelvir against Main Protease Mutants of SARS-CoV-2 Variants.
Biochemistry, 62, 2023
8HVM
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BU of 8hvm by Molmil
Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with PF07321332
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Wang, J, Zhang, J, Li, J.
登録日2022-12-27
公開日2023-12-27
最終更新日2025-07-09
実験手法X-RAY DIFFRACTION (1.48 Å)
主引用文献Evaluation of the Inhibition Potency of Nirmatrelvir against Main Protease Mutants of SARS-CoV-2 Variants.
Biochemistry, 62, 2023
8HVN
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BU of 8hvn by Molmil
Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with PF07321332
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Li, W.W, Zhang, J, Li, J.
登録日2022-12-27
公開日2023-12-27
最終更新日2025-07-09
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Evaluation of the Inhibition Potency of Nirmatrelvir against Main Protease Mutants of SARS-CoV-2 Variants.
Biochemistry, 62, 2023
8HVO
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BU of 8hvo by Molmil
Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with PF07321332
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Zou, X.F, Zhang, J, Li, J.
登録日2022-12-27
公開日2023-12-27
最終更新日2025-07-09
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献Evaluation of the Inhibition Potency of Nirmatrelvir against Main Protease Mutants of SARS-CoV-2 Variants.
Biochemistry, 62, 2023
8I4E
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BU of 8i4e by Molmil
Omicron spike variant XBB with Bn03
分子名称: Bn03, Spike glycoprotein
著者Hao, A.H, Zhang, X, Chen, Z.G, Sun, L.
登録日2023-01-19
公開日2023-12-27
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.98 Å)
主引用文献Defining a highly conserved cryptic epitope for antibody recognition of SARS-CoV-2 variants.
Signal Transduct Target Ther, 8, 2023
8I4F
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BU of 8i4f by Molmil
Omicron spike variant XBB with n3130v-Fc
分子名称: Spike glycoprotein, n3130v-Fc
著者Hao, A.H, Zhang, X, Chen, Z.G, Sun, L.
登録日2023-01-19
公開日2023-12-27
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Defining a highly conserved cryptic epitope for antibody recognition of SARS-CoV-2 variants.
Signal Transduct Target Ther, 8, 2023
8I4G
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BU of 8i4g by Molmil
Omicron spike variant BQ.1.1 with n3130v-Fc
分子名称: Spike glycoprotein, n3130v-Fc
著者Hao, A.H, Zhang, X, Chen, Z.G, Sun, L.
登録日2023-01-19
公開日2023-12-27
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.68 Å)
主引用文献Defining a highly conserved cryptic epitope for antibody recognition of SARS-CoV-2 variants.
Signal Transduct Target Ther, 8, 2023
8JJE
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BU of 8jje by Molmil
RBD of SARS-CoV2 spike protein with ACE2 decoy
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, Angiotensin-converting enzyme 2, ...
著者Kishikawa, J, Hirose, M, Kato, T, Okamoto, T.
登録日2023-05-30
公開日2023-12-27
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献An inhaled ACE2 decoy confers protection against SARS-CoV-2 infection in preclinical models.
Sci Transl Med, 15, 2023
8K5G
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BU of 8k5g by Molmil
Structure of the SARS-CoV-2 BA.1 RBD with UT28-RD
分子名称: Spike protein S1, UT28K-RD Fab Heavy chain, UT28K-RD Fab Light chain
著者Chen, L, Kita, S, Anraku, Y, Maenaka, K.
登録日2023-07-21
公開日2023-12-27
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.41 Å)
主引用文献Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1.
Structure, 32, 2024
8K5H
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BU of 8k5h by Molmil
Structure of the SARS-CoV-2 BA.1 spike with UT28-RD
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Chen, L, Kita, S, Anraku, Y, Maenaka, K.
登録日2023-07-21
公開日2023-12-27
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.22 Å)
主引用文献Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1.
Structure, 32, 2024
8TH1
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Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein D3L mutant
分子名称: Nucleoprotein, Ras GTPase-activating protein-binding protein 1
著者Hughes, M.P, Taylor, J.P, Yang, Z.
登録日2023-07-13
公開日2023-12-27
最終更新日2024-05-08
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity.
Cell Rep, 43, 2024
8IHO
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BU of 8iho by Molmil
Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors
分子名称: Papain-like protease nsp3, ZINC ION, covalent inhibitor
著者Wang, Q, Hu, H, Li, M, Xu, Y.
登録日2023-02-23
公開日2024-01-03
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2.55 Å)
主引用文献Structure-Based Design of Potent Peptidomimetic Inhibitors Covalently Targeting SARS-CoV-2 Papain-like Protease.
Int J Mol Sci, 24, 2023
8JYK
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BU of 8jyk by Molmil
Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 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Yajima, H, Anraku, Y, Kita, S, Kimura, K, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
登録日2023-07-03
公開日2024-01-03
最終更新日2025-01-15
実験手法ELECTRON MICROSCOPY (2.59 Å)
主引用文献Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant.
Nat Commun, 15, 2024
8JYN
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BU of 8jyn by Molmil
Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state)
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, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
登録日2023-07-03
公開日2024-01-03
最終更新日2025-01-15
実験手法ELECTRON MICROSCOPY (3.04 Å)
主引用文献Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant.
Nat Commun, 15, 2024
8FHY
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BU of 8fhy by Molmil
Crystal structure of the SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5021
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, MALONATE ION, ...
著者Sankhala, R.S, Jensen, J.L, Joyce, M.G.
登録日2022-12-15
公開日2024-01-17
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2.53 Å)
主引用文献Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques.
Nat Commun, 15, 2024
8FI9
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BU of 8fi9 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5001
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Spike protein S1, ...
著者Sankhala, R.S, Jensen, J.L, Joyce, M.G.
登録日2022-12-15
公開日2024-01-17
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (4.2 Å)
主引用文献Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques.
Nat Commun, 15, 2024

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件を2025-07-09に公開中

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