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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
8H91
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Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with nanobody N19
分子名称: Spike protein S1, nanobody
著者Zhang, Y.T, Li, J, Zhang, J.
登録日2022-10-24
公開日2023-11-01
実験手法X-RAY DIFFRACTION (3.07 Å)
主引用文献Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with nanobody N19
To Be Published
8PQ2
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XBB 1.0 RBD bound to P4J15 (Local)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, P4J15 Fragment Antigen-Binding Heavy Chain, P4J15 Fragment Antigen-Binding Light Chain, ...
著者Duhoo, Y, Lau, K.
登録日2023-07-10
公開日2023-11-01
最終更新日2023-12-06
実験手法ELECTRON MICROSCOPY (3.85 Å)
主引用文献Broadly potent anti-SARS-CoV-2 antibody shares 93% of epitope with ACE2 and provides full protection in monkeys.
J Infect, 87, 2023
8PSD
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SARS-CoV-2 XBB 1.0 closed conformation.
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Duhoo, Y, Lau, K.
登録日2023-07-13
公開日2023-11-01
最終更新日2023-12-06
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Broadly potent anti-SARS-CoV-2 antibody shares 93% of epitope with ACE2 and provides full protection in monkeys.
J Infect, 87, 2023
7GEF
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Group deposition SARS-CoV-2 main protease in complex with inhibitors from the COVID Moonshot -- Crystal Structure of SARS-CoV-2 main protease in complex with BEN-DND-93268d01-11 (Mpro-x11428)
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE, N-(4-methylpyridin-3-yl)-2-(piperidin-1-yl)acetamide
著者Fearon, D, Aimon, A, Aschenbrenner, J.C, Balcomb, B.H, Bertram, F.K.R, Brandao-Neto, J, Dias, A, Douangamath, A, Dunnett, L, Godoy, A.S, Gorrie-Stone, T.J, Koekemoer, L, Krojer, T, Lithgo, R.M, Lukacik, P, Marples, P.G, Mikolajek, H, Nelson, E, Owen, C.D, Powell, A.J, Rangel, V.L, Skyner, R, Strain-Damerell, C.M, Thompson, W, Tomlinson, C.W.E, Wild, C, Walsh, M.A, von Delft, F.
登録日2023-08-11
公開日2023-11-08
最終更新日2023-12-06
実験手法X-RAY DIFFRACTION (1.18 Å)
主引用文献Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.
Science, 382, 2023
7XQS
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The structure of FLA-K*00701/KP-CoV-9
分子名称: Beta-2-microglobulin, MHC class I antigen alpha chain, peptide from Spike glycoprotein
著者Qiao, P.W, Yue, C, Peng, W.Y, Liu, K.F, Huo, S.T, Zhang, D, Chai, Y, Qi, J.X, Sun, Z.Y, Gao, G.F, Liu, W.J, Wu, G.Z.
登録日2022-05-08
公開日2023-11-08
実験手法X-RAY DIFFRACTION (2.69 Å)
主引用文献Analysis of the characteristics of feline major histocompatibility complex class I molecules cross-presenting coronavirus peptides
To Be Published
8BG2
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Crystal structure of the SARS-CoV-2 S RBD in complex with pT1580 scFV
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, pT1375 single-chain Fv
著者Hansen, G, Ssebyatika, G.L, Krey, T.
登録日2022-10-27
公開日2023-11-08
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?
To be published
8BG3
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Crystal structure of the SARS-CoV-2 S RBD in complex with pT1610 scFV
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, pT1610 single-chain Fv
著者Hansen, G, Ssebyatika, G.L, Krey, T.
登録日2022-10-27
公開日2023-11-08
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?
To be published
8BG4
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Crystal structure of the SARS-CoV-2 S RBD in complex with pT1611 scFV
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, pT1611 single-chain Fv
著者Hansen, G, Ssebyatika, G.L, Krey, T.
登録日2022-10-27
公開日2023-11-08
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?
To be published
8BG5
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Crystal structure of the SARS-CoV-2 S RBD in complex with pT1631 scFV
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, pT1631 single-chain Fv
著者Hansen, G, Ssebyatika, G.L, Krey, T.
登録日2022-10-27
公開日2023-11-08
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?
To be published
8BG6
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BU of 8bg6 by Molmil
SARS-CoV-2 S protein in complex with pT1644 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, pT1644 Fab heavy chain, ...
著者Stroeh, L, Hansen, G, Vollmer, B, Krey, T, Benecke, T, Gruenewald, K.
登録日2022-10-27
公開日2023-11-08
実験手法ELECTRON MICROSCOPY (4.11 Å)
主引用文献Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?
To be published
8BG8
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SARS-CoV-2 S protein in complex with pT1696 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, pT1696 Fab heavy chain, ...
著者Hansen, G, Benecke, T, Vollmer, B, Gruenewald, K, Krey, T.
登録日2022-10-27
公開日2023-11-08
実験手法ELECTRON MICROSCOPY (3.64 Å)
主引用文献Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?
To be published
8HES
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BU of 8hes by Molmil
Crystal structure of SARS-CoV-2 RBD and NIV-10 complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-10 Fab H-chain, NIV-10 Fab L-chain, ...
著者Moriyama, S, Anraku, Y, Taminishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
登録日2022-11-08
公開日2023-11-08
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
7TPI
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SARS-CoV-2 E406W mutant Spike ectodomain
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Addetia, A, Veesler, D.
登録日2022-01-25
公開日2023-11-15
実験手法ELECTRON MICROSCOPY (2.3 Å)
主引用文献SARS-CoV-2 E406W mutant Spike ectodomain
To Be Published
8F4P
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SARS-CoV-2 spike protein trimer (down conformation) bound with a nanobody
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, Anti-S1 Nanobody, ...
著者Laughlin, Z.T, Patel, A, Ortlund, E.A.
登録日2022-11-11
公開日2023-11-15
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献SARS-CoV-2 spike protein (down conformation) bound with a nanobody
To Be Published
8IX3
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Cryo-EM structure of SARS-CoV-2 BA.4/5 spike protein in complex with 1G11 (local refinement)
分子名称: BA.4/5 variant spike protein, heavy chain of 1G11, light chain of 1G11
著者Sun, H, Jiang, Y, Zheng, Z, Zheng, Q, Li, S.
登録日2023-03-31
公開日2023-11-15
最終更新日2023-12-13
実験手法ELECTRON MICROSCOPY (3.98 Å)
主引用文献Structural basis for broad neutralization of human antibody against Omicron sublineages and evasion by XBB variant.
J.Virol., 97, 2023
8U1T
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SARS-CoV-2 Envelope Protein Transmembrane Domain: Dimeric Structure Determined by Solid-State NMR
分子名称: Envelope small membrane protein
著者Zhang, R, Qin, H, Prasad, R, Fu, R, Zhou, H.X, Cross, T.
登録日2023-09-02
公開日2023-11-15
最終更新日2024-05-15
実験手法SOLID-STATE NMR
主引用文献Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein.
Commun Biol, 6, 2023
8U28
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Gaussian mixture model based single particle refinement - SARS (SARS-CoV-2 Spike Proteins on intact virions from EMPIAR-10492)
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, M, Pintilie, G.
登録日2023-09-05
公開日2023-11-15
最終更新日2024-01-24
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models.
Nat.Methods, 21, 2024
8FIG
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Room-temperature X-ray structure of SARS-CoV-2 main protease double mutant E290A/R298A in complex with GC373
分子名称: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
著者Kovalevsky, A, Coates, L, Kneller, D.W.
登録日2022-12-16
公開日2023-11-22
実験手法X-RAY DIFFRACTION (1.75 Å)
主引用文献Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors.
Commun Biol, 6, 2023
8SQ9
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SARS-CoV-2 replication-transcription complex bound to nsp9 and UMPCPP, as a pre-catalytic NMPylation intermediate
分子名称: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine, MAGNESIUM ION, Non-structural protein 7, ...
著者Small, G.I, Darst, S.A, Campbell, E.A.
登録日2023-05-04
公開日2023-11-22
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.
Mol.Cell, 83, 2023
8SQJ
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SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, as a noncatalytic RNA-nsp9 binding mode
分子名称: 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine, MAGNESIUM ION, Non-structural protein 7, ...
著者Small, G.I, Darst, S.A, Campbell, E.A.
登録日2023-05-04
公開日2023-11-22
実験手法ELECTRON MICROSCOPY (3.06 Å)
主引用文献Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.
Mol.Cell, 83, 2023
8SQK
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SARS-CoV-2 replication-transcription complex bound to RNA-nsp9 and GDP-betaS, as a pre-catalytic deRNAylation/mRNA capping intermediate
分子名称: 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine, MAGNESIUM ION, Non-structural protein 7, ...
著者Small, G.I, Darst, S.A, Campbell, E.A.
登録日2023-05-04
公開日2023-11-22
実験手法ELECTRON MICROSCOPY (3.01 Å)
主引用文献Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.
Mol.Cell, 83, 2023
8X1H
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Crystal structure of N-terminal domain of Nucleocapsid protein of SARS-CoV-2
分子名称: GLYCEROL, Nucleoprotein
著者Kumari, S, Gupta, G.D.
登録日2023-11-07
公開日2023-11-22
最終更新日2024-07-03
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Unveiling potential inhibitors targeting the nucleocapsid protein of SARS-CoV-2: Structural insights into their binding sites.
Int.J.Biol.Macromol., 273, 2024
8I4S
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the complex structure of SARS-CoV-2 Mpro with D8
分子名称: 3-(4-fluoranyl-3-methyl-phenyl)-2-(2-methylpropyl)-5,6,7-tris(oxidanyl)quinazolin-4-one, ORF1a polyprotein
著者Lu, M.
登録日2023-01-21
公開日2023-11-29
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Discovery of quinazolin-4-one-based non-covalent inhibitors targeting the severe acute respiratory syndrome coronavirus 2 main protease (SARS-CoV-2 M pro ).
Eur.J.Med.Chem., 257, 2023
8J1T
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Local refined cryo-EM structure of Omicron BA.5 RBD in complex with 8-9D Fab
分子名称: 8-9D heavy chain, 8-9D light chain, Spike protein
著者Xiang, Y, Li, R.
登録日2023-04-13
公開日2023-11-29
最終更新日2023-12-20
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献A lung-selective delivery of mRNA encoding broadly neutralizing antibody against SARS-CoV-2 infection.
Nat Commun, 14, 2023
8J1V
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Cryo-EM structure of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 8-9D heavy chain, 8-9D light chain, ...
著者Xiang, Y, Li, R.
登録日2023-04-13
公開日2023-11-29
最終更新日2023-12-20
実験手法ELECTRON MICROSCOPY (3.01 Å)
主引用文献A lung-selective delivery of mRNA encoding broadly neutralizing antibody against SARS-CoV-2 infection.
Nat Commun, 14, 2023

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件を2024-07-17に公開中

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