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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
7X95
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BU of 7x95 by Molmil
The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab709
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Ab709 heavy chain, Ab709 light chain, ...
著者Kamada, K, Shirouzu, M.
登録日2022-03-15
公開日2023-03-22
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents.
Iscience, 26, 2023
7X96
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BU of 7x96 by Molmil
The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab847
分子名称: Ab847 heavy chain, Ab847 light chain, Spike glycoprotein, ...
著者Kamada, K, Shirouzu, M.
登録日2022-03-15
公開日2023-03-22
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents.
Iscience, 26, 2023
7XB4
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BU of 7xb4 by Molmil
Crystal structure of SARS-Cov-2 main protease D48N 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, Replicase polyprotein 1a
著者Hu, X.H, Li, J, Zhang, J.
登録日2022-03-20
公開日2023-03-22
最終更新日2024-10-02
実験手法X-RAY DIFFRACTION (2.07 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
7Z3U
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BU of 7z3u by Molmil
Crystal structure of SARS-CoV-2 Main Protease after incubation with Sulfo-Calpeptin
分子名称: 3C-like proteinase nsp5, CHLORIDE ION, Calpetin, ...
著者Reinke, P.Y.A, Falke, S, Lieske, J, Ewert, W, Loboda, J, Rahmani Mashhour, A, Hauser, M, Karnicar, K, Usenik, A, Lindic, N, Lach, M, Boehler, H, Beck, T, Cox, R, Chapman, H.N, Hinrichs, W, Turk, D, Guenther, S, Meents, A.
登録日2022-03-02
公開日2023-03-22
最終更新日2024-07-10
実験手法X-RAY DIFFRACTION (1.72 Å)
主引用文献Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.
Commun Biol, 6, 2023
7Z4S
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BU of 7z4s by Molmil
Crystal structure of SARS-CoV-2 Mpro in complex with cyclic peptide GM4 including unnatural amino acids.
分子名称: 1,2-ETHANEDIOL, 3C-like proteinase nsp5, DI(HYDROXYETHYL)ETHER, ...
著者Owen, C.D, Miura, T, Malla, T, Lukacik, L, Strain-Damerell, C.M, Tumber, A, Brewitz, L, McDonough, M.A, Salah, E, Terasaka, N, Katoh, T, Kawamura, A, Schofield, C.J, Suga, H, Walsh, M.A.
登録日2022-03-04
公開日2023-03-22
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献In vitro selection of macrocyclic peptide inhibitors containing cyclic gamma 2,4 -amino acids targeting the SARS-CoV-2 main protease.
Nat.Chem., 15, 2023
8BBN
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BU of 8bbn by Molmil
SARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs
分子名称: BA.2-10 heavy chain, BA.2-10 light chain, EY6A Heavy chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2022-10-14
公開日2023-03-22
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (3.58 Å)
主引用文献Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Cell Rep, 42, 2023
8BBO
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BU of 8bbo by Molmil
SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, IGH@ protein, Immunoglobulin kappa light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2022-10-14
公開日2023-03-22
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.75 Å)
主引用文献Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Cell Rep, 42, 2023
8BCZ
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BU of 8bcz by Molmil
SARS-CoV-2 Delta-RBD complexed with Fabs BA.2-36, BA.2-23, EY6A and COVOX-45
分子名称: BA.2-23 heavy chain, BA.2-23 light chain, BA.2-36 heavy chain, ...
著者Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
登録日2022-10-17
公開日2023-03-22
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Cell Rep, 42, 2023
8C3V
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BU of 8c3v by Molmil
SARS-CoV-2 Delta-RBD complexed with BA.2-13 Fab and C1 nanobody
分子名称: 2-(2-METHOXYETHOXY)ETHANOL, BA.2-13 heavy chain, BA.2-13 light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2022-12-28
公開日2023-03-22
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.74 Å)
主引用文献Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Cell Rep, 42, 2023
8D0Z
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BU of 8d0z by Molmil
S728-1157 IgG in complex with SARS-CoV-2-6P-Mut7 Spike protein (focused refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, S728-1157 Fab heavy chain variable region, S728-1157 Fab light chain variable region, ...
著者Ozorowski, G, Torres, J.L, Ward, A.B.
登録日2022-05-26
公開日2023-03-22
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants.
J.Clin.Invest., 133, 2023
8H3E
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BU of 8h3e by Molmil
Complex structure of a small molecule (SPC-14) bound SARS-CoV-2 spike protein, closed state
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 7-(6-nitro-2,3-dihydroindol-1-yl)-7-oxidanylidene-heptanoic acid, Spike glycoprotein,Fibritin
著者Meng, F, Wang, Q, Xie, Y, Ni, X, Huang, N.
登録日2022-10-08
公開日2023-03-22
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.06 Å)
主引用文献In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein.
Acs Cent.Sci., 9, 2023
8FA1
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BU of 8fa1 by Molmil
Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with N969K mutation
分子名称: Ferritin, Dps family protein and Spike protein S2' chimera, Spike protein S2' HR2
著者Yang, K, Brunger, A.T.
登録日2022-11-25
公開日2023-03-29
最終更新日2024-06-19
実験手法ELECTRON MICROSCOPY (2.51 Å)
主引用文献Structure-based design of a SARS-CoV-2 Omicron-specific inhibitor.
Proc.Natl.Acad.Sci.USA, 120, 2023
8FA2
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BU of 8fa2 by Molmil
Cryo-EM structure of the SARS-CoV-2 Omicron HR1-42G complex
分子名称: Scaffolded Spike protein S2' HR1, Spike protein S2' 42G
著者Yang, K, Brunger, A.T.
登録日2022-11-25
公開日2023-03-29
最終更新日2024-06-19
実験手法ELECTRON MICROSCOPY (2.82 Å)
主引用文献Structure-based design of a SARS-CoV-2 Omicron-specific inhibitor.
Proc.Natl.Acad.Sci.USA, 120, 2023
8EUA
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BU of 8eua by Molmil
Structure of SARS-CoV2 PLpro bound to a covalent inhibitor
分子名称: Papain-like protease nsp3, SULFATE ION, ZINC ION, ...
著者Mathews, I.I, Pokhrel, S, Wakatsuki, S.
登録日2022-10-18
公開日2023-04-05
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (3.1 Å)
主引用文献Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2.
Nat Commun, 14, 2023
8FU8
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BU of 8fu8 by Molmil
Structure of Covid Spike variant deltaN135 with one erect RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Yu, X, Juraszek, J, Rutten, L, Bakkers, M.J.G, Blokland, S, Van den Broek, N.J.F, Verwilligen, A.Y.W, Abeywickrema, P, Vingerhoets, J, Neefs, J, Bakhash, S.A.M, Roychoudhury, P, Greninger, A, Sharma, S, Langedijk, J.P.M.
登録日2023-01-16
公開日2023-04-05
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.08 Å)
主引用文献Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike.
Plos Pathog., 19, 2023
8FU9
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BU of 8fu9 by Molmil
Structure of Covid Spike variant deltaN25 with one erect RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Yu, X, Juraszek, J, Rutten, L, Bakkers, M.J.G, Blokland, S, Van den Broek, N.J.F, Verwilligen, A.Y.W, Abeywickrema, P, Vingerhoets, J, Neefs, J, Bakhash, S.A.M, Roychoudhury, P, Greninger, A, Sharma, S, Langedijk, J.P.M.
登録日2023-01-16
公開日2023-04-05
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.52 Å)
主引用文献Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike.
Plos Pathog., 19, 2023
8GJM
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17b10 fab in complex with full-length SARS-CoV-2 Spike G614 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Kwon, H.J, Zhang, J, Kosikova, M, Tang, W.C, Rodriguez, U.O, Peng, H.Q, Meseda, C.A, Pedro, C.L, Schmeisser, F, Lu, J.M, Zhou, B, Davis, C.T, Wentworth, D.E, Chen, W.H, Shriver, M.C, Pasetti, M.F, Weir, J.P, Chen, B, Xie, H.
登録日2023-03-16
公開日2023-04-05
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Distinct in vitro and in vivo neutralization profiles of monoclonal antibodies elicited by the receptor binding domain of the ancestral SARS-CoV-2.
J Med Virol, 95, 2023
8GJN
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BU of 8gjn by Molmil
17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 17B10 Fab, Light chain of 17B10 Fab, ...
著者Kwon, H.J, Zhang, J, Kosikova, M, Tang, W.C, Rodriguez, U.O, Peng, H.Q, Meseda, C.A, Pedro, C.L, Schmeisser, F, Lu, J.M, Zhou, B, Davis, C.T, Wentworth, D.E, Chen, W.H, Shriver, M.C, Pasetti, M.F, Weir, J.P, Chen, B, Xie, H.
登録日2023-03-16
公開日2023-04-05
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Distinct in vitro and in vivo neutralization profiles of monoclonal antibodies elicited by the receptor binding domain of the ancestral SARS-CoV-2.
J Med Virol, 95, 2023
8FEZ
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BU of 8fez by Molmil
Prefusion-stabilized SARS-CoV-2 spike protein
分子名称: Spike glycoprotein
著者Gonzalez, K.J, Mousa, J.J, Strauch, E.M.
登録日2022-12-07
公開日2023-04-12
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.72 Å)
主引用文献A general computational design strategy for stabilizing viral class I fusion proteins.
Nat Commun, 15, 2024
8GZZ
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BU of 8gzz by Molmil
Local refinement of SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab
分子名称: Spike protein S1, rabbit monoclonal antibody 1H1 Fab heavy chain, rabbit monoclonal antibody 1H1 Fab light chain
著者Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
登録日2022-09-27
公開日2023-04-12
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.52 Å)
主引用文献Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants.
Commun Biol, 6, 2023
8H00
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BU of 8h00 by Molmil
SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab in the class 1 conformation
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, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
登録日2022-09-27
公開日2023-04-12
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.41 Å)
主引用文献Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants.
Commun Biol, 6, 2023
7WN2
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BU of 7wn2 by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab Heavy chain, Fab Light chain, ...
著者Yamamoto, A, Higashiura, A.
登録日2022-01-17
公開日2023-04-19
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol, 6, 2023
7WNB
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BU of 7wnb by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab Heavy chain, Fab Light chain, ...
著者Yamamoto, A, Higashiura, A.
登録日2022-01-18
公開日2023-04-19
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.18 Å)
主引用文献Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol, 6, 2023
7XJ6
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BU of 7xj6 by Molmil
SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 1 conformation
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, 55A8 heavy chain, ...
著者Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
登録日2022-04-15
公開日2023-04-19
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.29 Å)
主引用文献SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 1 conformation
To Be Published
7XJ8
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SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 2 conformation
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, 55A8 heavy chain, ...
著者Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
登録日2022-04-15
公開日2023-04-19
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 2 conformation
To Be Published

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件を2025-07-09に公開中

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