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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
7QF1
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Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.6264
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CV2.6264 heavy chain, CV2.6264 light chain, ...
著者Fernandez, I, Pederzoli, R, Rey, F.A.
登録日2021-12-03
公開日2022-05-18
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2.
J.Exp.Med., 219, 2022
7WG6
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Neutral Omicron Spike Trimer
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Cui, Z, Wang, X.
登録日2021-12-28
公開日2022-05-18
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron.
Cell, 185, 2022
7ZDQ
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Cryo-EM structure of Human ACE2 bound to a high-affinity SARS CoV-2 mutant
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1
著者Bate, N, Savva, C.G, Moody, P.C.E, Brown, E.A, Schwabe, W.R, Brindle, N.P.J, Ball, J.K, Sale, J.E.
登録日2022-03-29
公開日2022-05-18
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献In vitro evolution predicts emerging SARS-CoV-2 mutations with high affinity for ACE2 and cross-species binding.
Plos Pathog., 18, 2022
7F5G
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The crystal structure of RBD-Nanobody complex, DL4 (SA4)
分子名称: ACETATE ION, GLYCEROL, Nanobody DL4, ...
著者Li, T, Lai, Y, Zhou, Y, Tan, J, Li, D.
登録日2021-06-22
公開日2022-05-25
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (1.75 Å)
主引用文献Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2.
Int.J.Biol.Macromol., 209, 2022
7MXP
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Cryo-EM structure of NTD-directed neutralizing antibody LP5 Fab in complex with SARS-CoV-2 S2P spike
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)][beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Reddem, E.R, Casner, R.G, Shapiro, L.
登録日2021-05-19
公開日2022-05-25
最終更新日2025-06-04
実験手法ELECTRON MICROSCOPY (4.46 Å)
主引用文献Antibody screening at reduced pH enables preferential selection of potently neutralizing antibodies targeting SARS-CoV-2.
Aiche J, 67, 2021
7QDG
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SARS-CoV-2 S protein S:A222V + S:D614G mutant 1-up
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Ginex, T, Marco-Marin, C, Wieczor, M, Mata, C.P, Krieger, J, Lopez-Redondo, M.L, Frances-Gomez, C, Ruiz-Rodriguez, P, Melero, R, Sanchez-Sorzano, C.O, Martinez, M, Gougeard, N, Forcada-Nadal, A, Zamora-Caballero, S, Gozalbo-Rovira, R, Sanz-Frasquet, C, Bravo, J, Rubio, V, Marina, A, Geller, R, Comas, I, Gil, C, Coscolla, M, Orozco, M, LLacer, J.L, Carazo, J.M.
登録日2021-11-27
公開日2022-05-25
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.
Plos Pathog., 18, 2022
7QDH
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SARS-CoV-2 S protein S:D614G mutant 1-up
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,Fibritin
著者Ginex, T, Marco-Marin, C, Wieczor, M, Mata, C.P, Krieger, J, Lopez-Redondo, M.L, Frances-Gomez, C, Ruiz-Rodriguez, P, Melero, R, Sanchez-Sorzano, C.O, Martinez, M, Gougeard, N, Forcada-Nadal, A, Zamora-Caballero, S, Gozalbo-Rovira, R, Sanz-Frasquet, C, Bravo, J, Rubio, V, Marina, A, Geller, R, Comas, I, Gil, C, Coscolla, M, Orozco, M, LLacer, J.L, Carazo, J.M.
登録日2021-11-27
公開日2022-05-25
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (4.2 Å)
主引用文献The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.
Plos Pathog., 18, 2022
7WLZ
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Cryo-EM structure of the Omicron S in complex with 35B5 Fab(1 down-, 1 up- and 1 invisible RBDs)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 35B5 Fab, Light chain of 35B5 Fab, ...
著者Wang, X, Zhu, Y.
登録日2022-01-14
公開日2022-05-25
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (2.98 Å)
主引用文献35B5 antibody potently neutralizes SARS-CoV-2 Omicron by disrupting the N-glycan switch via a conserved spike epitope.
Cell Host Microbe, 30, 2022
7X7O
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SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K
分子名称: Spike protein S1, UT28K Fab, heavy chain, ...
著者Ozawa, T, Tani, H, Anraku, Y, Kita, S, Igarashi, E, Saga, Y, Inasaki, N, Kawasuji, H, Yamada, H, Sasaki, S, Somekawa, M, Sasaki, J, Hayakawa, Y, Yamamoto, Y, Morinaga, Y, Kurosawa, N, Isobe, M, Fukuhara, H, Maenaka, K, Hashiguchi, T, Kishi, H, Kitajima, I, Saito, S, Niimi, H.
登録日2022-03-10
公開日2022-05-25
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (3.75 Å)
主引用文献Novel super-neutralizing antibody UT28K is capable of protecting against infection from a wide variety of SARS-CoV-2 variants.
Mabs, 14, 2022
7FAU
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Structure Determination of the NB1B11-RBD Complex
分子名称: NB_1B11, Spike protein S1, ZINC ION
著者Shi, Z.Z, Li, X.X, Wang, L, Sun, Z.C, Zhang, H.W, Chen, X.C, Cui, Q.Q, Qiao, H.R, Lan, Z.Y, Zhang, X.
登録日2021-07-07
公開日2022-06-01
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2.08 Å)
主引用文献Structural basis of nanobodies neutralizing SARS-CoV-2 variants.
Structure, 30, 2022
7QUR
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SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry
分子名称: 2,3,5-tris(iodanyl)benzamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Naismith, J.H, Yang, Y, Liu, J.W.
登録日2022-01-18
公開日2022-06-01
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.27 Å)
主引用文献Pathogen-sugar interactions revealed by universal saturation transfer analysis.
Science, 377, 2022
7WHH
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Crystal structure of SARS-CoV-2 omicron RBD and human ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Processed angiotensin-converting enzyme 2, ...
著者Wang, X.Q, Lan, J.
登録日2021-12-30
公開日2022-06-01
最終更新日2025-06-18
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction.
Cell Res., 32, 2022
7WS0
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BU of 7ws0 by Molmil
Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
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, 510A5 heavy chain, ...
著者Guo, H, Gao, Y, Ji, X, Yang, H.
登録日2022-01-28
公開日2022-06-01
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structures of Omicron spike complexes and implications for neutralizing antibody development.
Cell Rep, 39, 2022
7WS2
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Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
分子名称: 510A5 heavy chain, 510A5 light chain, Spike protein S1
著者Guo, H, Gao, Y, Ji, X, Yang, H.
登録日2022-01-28
公開日2022-06-01
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Structures of Omicron spike complexes and implications for neutralizing antibody development.
Cell Rep, 39, 2022
7WS3
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BU of 7ws3 by Molmil
Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
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, 510A5 heavy chain, ...
著者Guo, H, Gao, Y, Ji, X, Yang, H.
登録日2022-01-28
公開日2022-06-01
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Structures of Omicron spike complexes and implications for neutralizing antibody development.
Cell Rep, 39, 2022
7WS5
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Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
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, 510A5 heavy chain, ...
著者Guo, H, Gao, Y, Ji, X, Yang, H.
登録日2022-01-28
公開日2022-06-01
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Structures of Omicron spike complexes and implications for neutralizing antibody development.
Cell Rep, 39, 2022
7WS6
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Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
分子名称: 510A5 heavy chain, 510A5 light chain, Spike protein S1
著者Guo, H, Gao, Y, Ji, X, Yang, H.
登録日2022-01-28
公開日2022-06-01
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Structures of Omicron spike complexes and implications for neutralizing antibody development.
Cell Rep, 39, 2022
7WS7
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BU of 7ws7 by Molmil
Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 510A5 heavy chain, 510A5 light chain, ...
著者Guo, H, Gao, Y, Ji, X, Yang, H.
登録日2022-01-28
公開日2022-06-01
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Structures of Omicron spike complexes and implications for neutralizing antibody development.
Cell Rep, 39, 2022
7WS9
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BU of 7ws9 by Molmil
Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
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Guo, H, Gao, Y, Ji, X, Yang, H.
登録日2022-01-28
公開日2022-06-01
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Structures of Omicron spike complexes and implications for neutralizing antibody development.
Cell Rep, 39, 2022
7WSA
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Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1
著者Guo, H, Gao, Y, Ji, X, Yang, H.
登録日2022-01-28
公開日2022-06-01
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structures of Omicron spike complexes and implications for neutralizing antibody development.
Cell Rep, 39, 2022
7WWL
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S protein of Delta variant in complex with ZWD12
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Guo, Y.Y, Zhang, Y.Y, Zhou, Q.
登録日2022-02-13
公開日2022-06-01
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Broadly neutralizing antibodies against Omicron-included SARS-CoV-2 variants induced by vaccination.
Signal Transduct Target Ther, 7, 2022
7WWM
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S protein of Delta variant in complex with ZWC6
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Guo, Y.Y, Zhang, Y.Y, Zhou, Q.
登録日2022-02-13
公開日2022-06-01
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Broadly neutralizing antibodies against Omicron-included SARS-CoV-2 variants induced by vaccination.
Signal Transduct Target Ther, 7, 2022
7ZB6
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant C44S at 2.12 A resolution
分子名称: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
著者Paknia, E, Rabe von Pappenheim, F, Funk, L.-M, Tittmann, K, Chari, A.
登録日2022-03-23
公開日2022-06-01
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.12 Å)
主引用文献Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design.
Nat Commun, 15, 2024
7ZB7
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant Y54F at 1.63 A resolution
分子名称: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, GLYCEROL
著者Paknia, E, Rabe von Pappenheim, F, Funk, L.-M, Tittmann, K, Chari, A.
登録日2022-03-23
公開日2022-06-01
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.63 Å)
主引用文献Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design.
Nat Commun, 15, 2024
7ZB8
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant K61A at 2.48 A resolution
分子名称: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
著者Paknia, E, Rabe von Pappenheim, F, Funk, L.-M, Tittmann, K, Chari, A.
登録日2022-03-23
公開日2022-06-01
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.48 Å)
主引用文献Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design.
Nat Commun, 15, 2024

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件を2025-07-09に公開中

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