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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
7DK7
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BU of 7dk7 by Molmil
S-2H2-F3b structure, three RBDs are up and each RBD binds with a 2H2 Fab.
分子名称: Spike glycoprotein, The heavy chain fragment of 2H2 Fab, The light chain fragment of 2H2 Fab
著者Cong, Y, Wang, Y.F.
登録日2020-11-23
公開日2020-12-02
最終更新日2021-03-10
実験手法ELECTRON MICROSCOPY (9.7 Å)
主引用文献Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections.
Nat Commun, 12, 2021
7JQB
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BU of 7jqb by Molmil
SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
分子名称: 40S ribosomal protein S21, 40S ribosomal protein S24, 40S ribosomal protein S26, ...
著者Yuan, S, Xiong, Y.
登録日2020-08-10
公開日2020-12-02
最終更新日2024-03-06
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.
Mol.Cell, 80, 2020
7JQC
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BU of 7jqc by Molmil
SARS-CoV-2 Nsp1, CrPV IRES and rabbit 40S ribosome complex
分子名称: 40S ribosomal protein S21, 40S ribosomal protein S24, 40S ribosomal protein S26, ...
著者Yuan, S, Xiong, Y.
登録日2020-08-10
公開日2020-12-02
最終更新日2024-03-06
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.
Mol.Cell, 80, 2020
7JVB
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BU of 7jvb by Molmil
Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20
分子名称: CACODYLATE ION, Nanobody Nb20, Spike protein S1
著者Xiang, Y, Xiao, Z, Liu, H, Sang, Z, Schneidman-Duhovny, D, Zhang, C, Shi, Y.
登録日2020-08-20
公開日2020-12-02
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3.287 Å)
主引用文献Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2.
Science, 370, 2020
7KEG
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BU of 7keg by Molmil
Crystal structure from SARS-COV2 NendoU NSP15
分子名称: PHOSPHATE ION, Uridylate-specific endoribonuclease
著者Godoy, A.S, Nakamura, A.M, Pereira, H.M, Noske, G.D, Gawriljuk, V.O, Fernandes, R.S, Oliveira, K.I.Z, Oliva, G.
登録日2020-10-10
公開日2020-12-02
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.
Nucleic Acids Res., 2023
7KEH
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BU of 7keh by Molmil
Crystal structure from SARS-CoV-2 NendoU NSP15
分子名称: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, SULFATE ION, Uridylate-specific endoribonuclease
著者Godoy, A.S, Nakamura, A.M, Pereira, H.M, Noske, G.D, Gawriljuk, V.O, Fernandes, R.S, Oliveira, K.I.Z, Oliva, G.
登録日2020-10-10
公開日2020-12-02
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.59 Å)
主引用文献Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.
Nucleic Acids Res., 2023
7KF4
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Crystal structure from SARS-CoV-2 NendoU NSP15
分子名称: CITRIC ACID, Uridylate-specific endoribonuclease
著者Godoy, A.S, Nakamura, A.M, Pereira, H.M, Noske, G.D, Gawriljuk, V.O, Fernandes, R.S, Oliveira, K.I.Z, Oliva, G.
登録日2020-10-13
公開日2020-12-02
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.61 Å)
主引用文献Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.
Nucleic Acids Res., 2023
7KFV
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BU of 7kfv by Molmil
Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B12 Fab)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of antibody C1A-B12 Fab, Spike glycoprotein, ...
著者Pan, J, Abraham, J, Clark, L, Clark, S.
登録日2020-10-15
公開日2020-12-02
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.102 Å)
主引用文献Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.
Biorxiv, 2020
7KFW
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BU of 7kfw by Molmil
Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B3 Fab)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, heavy chain of antibody C1A-B3 Fab, ...
著者Pan, J, Abraham, J, Clark, L, Clark, S.
登録日2020-10-15
公開日2020-12-02
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.792 Å)
主引用文献Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.
Biorxiv, 2020
7KFX
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BU of 7kfx by Molmil
Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 Fab)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, heavy chain of human antibody C1A-C2 Fab, ...
著者Pan, J, Abraham, J, Clark, L, Clark, S.
登録日2020-10-15
公開日2020-12-02
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.226 Å)
主引用文献Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.
Biorxiv, 2020
7KFY
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BU of 7kfy by Molmil
Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-F10 Fab)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, heavy chain of human antibody C1A-F10 Fab, ...
著者Pan, J, Abraham, J, Clark, L, Clark, S.
登録日2020-10-15
公開日2020-12-02
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.157 Å)
主引用文献Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.
Biorxiv, 2020
7KRX
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BU of 7krx by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder441 inhibitor
分子名称: 3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ACETATE ION, CHLORIDE ION, ...
著者Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-11-20
公開日2020-12-02
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.72 Å)
主引用文献The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder441
to be published
7CYQ
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BU of 7cyq by Molmil
Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis
分子名称: GUANOSINE-5'-DIPHOSPHATE, Helicase, MAGNESIUM ION, ...
著者Yan, L, Ge, J, Zheng, L, Zhang, Y, Gao, Y, Wang, T, Wang, H, Huang, Y, Li, M, Wang, Q, Rao, Z, Lou, Z.
登録日2020-09-04
公開日2020-12-09
最終更新日2024-03-27
実験手法ELECTRON MICROSCOPY (2.83 Å)
主引用文献Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis.
Cell, 184, 2021
7K0R
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BU of 7k0r by Molmil
Nucleotide bound SARS-CoV-2 Nsp15
分子名称: PHOSPHATE ION, URIDINE-5'-MONOPHOSPHATE, Uridylate-specific endoribonuclease
著者Pillon, M.C, Stanley, R.E.
登録日2020-09-04
公開日2020-12-09
最終更新日2024-03-06
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics.
Nat Commun, 12, 2021
7KMB
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ACE2-RBD Focused Refinement Using Symmetry Expansion of Applied C3 for Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4
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, Angiotensin-converting enzyme 2, ...
著者Gorman, J, Kwong, P.D, Shapiro, L.
登録日2020-11-02
公開日2020-12-09
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (3.39 Å)
主引用文献Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cell Host Microbe, 28, 2020
7KMS
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BU of 7kms by Molmil
Cryo-EM structure of triple ACE2-bound SARS-CoV-2 trimer spike at pH 7.4
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, Angiotensin-converting enzyme 2, ...
著者Gorman, J, Kwong, P.D, Shapiro, L.
登録日2020-11-03
公開日2020-12-09
最終更新日2021-12-15
実験手法ELECTRON MICROSCOPY (3.64 Å)
主引用文献Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cell Host Microbe, 28, 2020
7KMZ
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BU of 7kmz by Molmil
Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4
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, Angiotensin-converting enzyme 2, ...
著者Gorman, J, Kwong, P.D, Shapiro, L.
登録日2020-11-03
公開日2020-12-09
最終更新日2021-12-15
実験手法ELECTRON MICROSCOPY (3.62 Å)
主引用文献Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cell Host Microbe, 28, 2020
7KNB
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BU of 7knb by Molmil
Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 7.4
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, Angiotensin-converting enzyme 2, ...
著者Gorman, J, Kwong, P.D, Shapiro, L.
登録日2020-11-04
公開日2020-12-09
最終更新日2021-12-15
実験手法ELECTRON MICROSCOPY (3.93 Å)
主引用文献Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cell Host Microbe, 28, 2020
7KQO
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BU of 7kqo by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain (P43 crystal form)
分子名称: Non-structural protein 3
著者Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
登録日2020-11-17
公開日2020-12-09
最終更新日2024-03-06
実験手法X-RAY DIFFRACTION (0.85 Å)
主引用文献Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
7KQP
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BU of 7kqp by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal form)
分子名称: Non-structural protein 3, [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
著者Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
登録日2020-11-17
公開日2020-12-09
最終更新日2024-03-06
実験手法X-RAY DIFFRACTION (0.88 Å)
主引用文献Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
7KQW
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BU of 7kqw by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, methylated)
分子名称: Non-structural protein 3
著者Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
登録日2020-11-17
公開日2020-12-09
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (0.93 Å)
主引用文献Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
7KR0
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BU of 7kr0 by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
分子名称: Non-structural protein 3
著者Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
登録日2020-11-18
公開日2020-12-09
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (0.77 Å)
主引用文献Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
7KR1
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BU of 7kr1 by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 310 K)
分子名称: Non-structural protein 3
著者Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
登録日2020-11-18
公開日2020-12-09
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
7KVL
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BU of 7kvl by Molmil
SARS-CoV-2 Main protease immature form - FMAX Library E01 fragment
分子名称: 2-chloropyridine-4-carboxamide, 3C-like proteinase, DI(HYDROXYETHYL)ETHER, ...
著者Noske, G.D, Nakamura, A.M, Gawriljuk, V.O, Lima, G.M.A, Zeri, A.C.M, Nascimento, A.F.Z, Fernandes, R.S, Oliva, G, Godoy, A.S.
登録日2020-11-28
公開日2020-12-09
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.09 Å)
主引用文献A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.
J.Mol.Biol., 433, 2021
7KVR
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BU of 7kvr by Molmil
SARS-CoV-2 Main protease immature form - FMAX Library E09 fragment
分子名称: 3C-like proteinase, DI(HYDROXYETHYL)ETHER, DIMETHYL SULFOXIDE, ...
著者Noske, G.D, Nakamura, A.M, Gawriljuk, V.O, Lima, G.M.A, Zeri, A.C.M, Nascimento, A.F.Z, Fernandes, R.S, Oliva, G, Godoy, A.S.
登録日2020-11-28
公開日2020-12-09
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.12 Å)
主引用文献A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.
J.Mol.Biol., 433, 2021

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件を2024-06-12に公開中

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