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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
7QEZ
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BU of 7qez by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with the ultrapotent antibody CV2.1169 and CR3022
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 heavy chain, CR3022 light chain, ...
著者Fernandez, I, Rey, F.A.
登録日2021-12-03
公開日2022-05-18
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (2.89 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
7QF0
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Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.2325
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, CV2.2325 heavy 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2024-02-07
実験手法X-RAY DIFFRACTION (2.3 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
7QF1
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BU of 7qf1 by Molmil
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2024-02-07
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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BU of 7wg6 by Molmil
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2022-07-20
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2022-08-10
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2023-11-29
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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BU of 7mxp by Molmil
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2022-12-21
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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BU of 7qdg by Molmil
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2022-08-24
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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BU of 7qdh by Molmil
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2022-08-10
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
7WLY
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BU of 7wly by Molmil
Cryo-EM structure of the Omicron S in complex with 35B5 Fab(1 down- and 2 up RBDs)
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, Heavy 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2022-06-22
実験手法ELECTRON MICROSCOPY (3.4 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
7WLZ
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BU of 7wlz by Molmil
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2022-06-22
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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BU of 7x7o by Molmil
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2023-11-29
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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BU of 7fau by Molmil
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2023-11-29
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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BU of 7qur by Molmil
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2022-08-03
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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BU of 7whh by Molmil
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2023-11-29
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Crystal structure of SARS-CoV-2 omicron RBD and human ACE2
To Be Published
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
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
7WS1
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BU of 7ws1 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
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
7WS2
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BU of 7ws2 by Molmil
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
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
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
7WS4
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BU of 7ws4 by Molmil
Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants
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
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
7WS5
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BU of 7ws5 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
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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BU of 7ws6 by Molmil
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
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
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
7WS8
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BU of 7ws8 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
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
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
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

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件を2024-07-10に公開中

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