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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
8F0H
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BU of 8f0h by Molmil
Structure of SARS-CoV-2 spike with antibody Fabs 2A10 and 1H2 (Local refinement of the RBD and Fabs 1H2 and 2A10)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody Fab 1H2 heavy chain, Antibody Fab 1H2 light chain, ...
著者Yu, X, Zyla, D, Hastie, K.M, Saphire, E.O.
登録日2022-11-02
公開日2023-05-03
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.18 Å)
主引用文献Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.
Cell Rep, 42, 2023
8GS9
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BU of 8gs9 by Molmil
SARS-CoV-2 BA.2 spike RBD in complex bound with VacBB-551
分子名称: Heavy chain of VacBB-551, Light chain of VacBB-551, Spike glycoprotein
著者Liu, C.C, Ju, B, Shen, S.L, Zhang, Z.
登録日2022-09-05
公開日2023-05-03
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (2.66 Å)
主引用文献Omicron BQ.1.1 and XBB.1 unprecedentedly escape broadly neutralizing antibodies elicited by prototype vaccination.
Cell Rep, 42, 2023
7XSA
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BU of 7xsa by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P2S-2E9 Fab
分子名称: P2S-2E9 Heavy chain, P2S-2E9 Light chain, Spike protein S1
著者Wang, X, Wang, Z.
登録日2022-05-13
公開日2023-05-10
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
7XSB
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BU of 7xsb by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab
分子名称: P5S-3B11 Heavy chain, P5S-3B11 Light chain, Spike protein S1
著者Wang, X, Wang, Z, Gao, M.
登録日2022-05-13
公開日2023-05-10
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
8A99
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BU of 8a99 by Molmil
SARS Cov2 Spike in 1-up conformation complex with Fab47
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, Fab47 (Heavy chain variable domain), ...
著者Hallberg, B.M, Das, H.
登録日2022-06-28
公開日2023-05-10
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (2.5 Å)
主引用文献Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies.
Immunity, 56, 2023
8H3M
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BU of 8h3m by Molmil
Conformation 1 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy chain, Spike glycoprotein
著者Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y.
登録日2022-10-09
公開日2023-05-10
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (2.48 Å)
主引用文献Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
8H3N
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BU of 8h3n by Molmil
Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy-chain, MO1 light chain, ...
著者Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y.
登録日2022-10-09
公開日2023-05-10
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (2.73 Å)
主引用文献Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
8OT0
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SARS-CoV-2 nsp10-16 methyltransferase in complex with MTA and glycine
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D, Falke, S.
登録日2023-04-20
公開日2023-05-10
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.21 Å)
主引用文献SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery
Elife, 2024
8OV1
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BU of 8ov1 by Molmil
SARS-CoV-2 nsp10-16 methyltransferase in complex with ADP
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D.
登録日2023-04-25
公開日2023-05-10
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.67 Å)
主引用文献SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery
Elife, 2024
8BSE
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BU of 8bse by Molmil
CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab
分子名称: 1D1 FAB HEAVY CHAIN, 1D1 FAB LIGHT CHAIN, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ...
著者Welin, M, Kimbung, Y.R, Focht, D, Pisitkun, T.
登録日2022-11-25
公開日2023-05-17
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants.
Plos One, 18, 2023
8BSF
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BU of 8bsf by Molmil
CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 3D2 FAB HEAVY CHAIN, 3D2 FAB LIGHT CHAIN, ...
著者Welin, M, Kimbung, Y.R, Focht, D, Pisitkun, T.
登録日2022-11-25
公開日2023-05-17
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants.
Plos One, 18, 2023
8CSJ
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BU of 8csj by Molmil
Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein
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-(2-3)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Reddem, E.R, Shapiro, L.
登録日2022-05-12
公開日2023-05-17
最終更新日2025-06-04
実験手法ELECTRON MICROSCOPY (3.53 Å)
主引用文献Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein
To Be Published
8FWN
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BU of 8fwn by Molmil
Crystal structure of SARS-CoV-2 papain-like protease C111S mutant
分子名称: ACETATE ION, CHLORIDE ION, GLYCEROL, ...
著者Bezerra, E.H.S, Soprano, A.S, Tonoli, C.C.C, Prado, P.F.V, da Silva, J.C, Franchini, K.G, Trivella, D.B.B, Benedetti, C.E.
登録日2023-01-23
公開日2023-05-17
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Crystal structure of SARS-CoV-2 papain-like protease C111S mutant
To Be Published
8HN6
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BU of 8hn6 by Molmil
Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD
分子名称: Heavy chain of monoclonal antibody 3G10, Light chain of monoclonal antibody 3G10, Spike protein S1
著者Qi, J, Chen, Y.
登録日2022-12-07
公開日2023-05-17
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.07 Å)
主引用文献Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.
Front Immunol, 14, 2023
8HN7
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BU of 8hn7 by Molmil
Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of monoclonal antibody 3C11, Light chain of monoclonal antibody 3C11, ...
著者Qi, J, Chen, Y.
登録日2022-12-07
公開日2023-05-17
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.
Front Immunol, 14, 2023
8IF2
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BU of 8if2 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor ACE2
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Kimura, K, Suzuki, T, Hashiguchi, T.
登録日2023-02-17
公開日2023-05-17
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2.78 Å)
主引用文献Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
Nat Commun, 14, 2023
7XSC
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BU of 7xsc by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-2B10
分子名称: P5S-2B10 Heavy chain, P5S-2B10 Light chain, Spike protein S1
著者Wang, X, Wang, Z, Lin, Z.
登録日2022-05-13
公開日2023-05-24
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.88 Å)
主引用文献Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
8CWI
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BU of 8cwi by Molmil
Fab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Heavy chain of Fab arm of antibody 10G4, ...
著者Langley, D.B, Christ, D.
登録日2022-05-19
公開日2023-05-24
最終更新日2025-01-15
実験手法X-RAY DIFFRACTION (1.873 Å)
主引用文献Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies.
Proc.Natl.Acad.Sci.USA, 122, 2025
8CWK
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BU of 8cwk by Molmil
Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Heavy chain of Fab arm of antibody 10G4, ...
著者Langley, D.B, Christ, D.
登録日2022-05-19
公開日2023-05-24
最終更新日2025-01-15
実験手法X-RAY DIFFRACTION (2.368 Å)
主引用文献Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies.
Proc.Natl.Acad.Sci.USA, 122, 2025
8DNN
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BU of 8dnn by Molmil
Crystal structure of neutralizing antibody 80 in complex with SARS-CoV-2 receptor binding domain
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 80 FAB HEAVY CHAIN, 80 FAB LIGHT CHAIN, ...
著者Muthuraman, K, Kucharska, I, Ivanochko, D, Julien, J.P.
登録日2022-07-11
公開日2023-05-24
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (3.12 Å)
主引用文献A multi-specific, multi-affinity antibody platform neutralizes sarbecoviruses and confers protection against SARS-CoV-2 in vivo.
Sci Transl Med, 15, 2023
8GB5
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BU of 8gb5 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9
分子名称: 25F9 Heavy chain, 25F9 Light chain, BICINE, ...
著者Yuan, M, Zhu, X, Wilson, I.A.
登録日2023-02-24
公開日2023-05-24
最終更新日2024-12-25
実験手法X-RAY DIFFRACTION (3.35 Å)
主引用文献Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB6
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BU of 8gb6 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 21B6
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, 21B6 Heavy chain, 21B6 Light chain, ...
著者Yuan, M, Wilson, I.A.
登録日2023-02-24
公開日2023-05-24
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.75 Å)
主引用文献Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB7
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BU of 8gb7 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 20A7
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 20A7 Heavy chain, 20A7 Light chain, ...
著者Yuan, M, Wilson, I.A.
登録日2023-02-24
公開日2023-05-24
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.57 Å)
主引用文献Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB8
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BU of 8gb8 by Molmil
Crystal structure of SARS-CoV-2 BA.2 receptor binding domain in complex with neutralizing antibody 20A7
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 20A7 Heavy chain, ...
著者Yuan, M, Wilson, I.A.
登録日2023-02-24
公開日2023-05-24
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8ILC
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BU of 8ilc by Molmil
Crystal structure of Se-Met CoV-Y domain of Nsp3 in SARS-CoV-2
分子名称: CHLORIDE ION, Papain-like protease nsp3, SULFATE ION
著者Wang, K, Nan, J, Lei, J.
登録日2023-03-03
公開日2023-05-24
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献The CoV-Y domain of SARS-CoV-2 Nsp3 interacts with BRAP to stimulate NF-kappa B signaling and induce host inflammatory responses.
Int.J.Biol.Macromol., 280, 2024

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件を2025-07-09に公開中

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