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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
6WEY
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BU of 6wey by Molmil
High-resolution structure of the SARS-CoV-2 NSP3 Macro X domain
分子名称: Non-structural protein 3
著者Vuksanovic, N, Silvaggi, N.R.
登録日2020-04-03
公開日2020-04-29
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (0.95 Å)
主引用文献Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3.
Biochemistry, 59, 2020
6WKP
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BU of 6wkp by Molmil
Crystal structure of RNA-binding domain of nucleocapsid phosphoprotein from SARS CoV-2, monoclinic crystal form
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Nucleoprotein, ZINC ION
著者Chang, C, Michalska, K, Jedrzejczak, R, Maltseva, N, Endres, M, Godzik, A, Kim, Y, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-04-16
公開日2020-04-29
最終更新日2024-02-28
実験手法X-RAY DIFFRACTION (2.67 Å)
主引用文献Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
Iscience, 27, 2024
6WLC
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BU of 6wlc by Molmil
Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-5'-Monophosphate
分子名称: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, ...
著者Kim, Y, Maltseva, N, Jedrzejczak, R, Endres, M, Chang, C, Godzik, A, Michalska, K, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-04-19
公開日2020-04-29
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.82 Å)
主引用文献Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.
Commun Biol, 4, 2021
6YHU
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BU of 6yhu by Molmil
Crystal structure of the nsp7-nsp8 complex of SARS-CoV-2
分子名称: Replicase polyprotein 1a
著者Konkolova, E, Klima, M, Boura, E.
登録日2020-03-31
公開日2020-04-29
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Structural analysis of the putative SARS-CoV-2 primase complex.
J.Struct.Biol., 211, 2020
6YM0
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BU of 6ym0 by Molmil
Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab (crystal form 1)
分子名称: Spike glycoprotein, heavy chain, light chain
著者Huo, J, Zhao, Y, Ren, J, Zhou, D, Ginn, H.M, Fry, E.E, Owens, R, Stuart, D.I.
登録日2020-04-07
公開日2020-04-29
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (4.36 Å)
主引用文献Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.
Cell Host Microbe, 28, 2020
6YOR
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BU of 6yor by Molmil
Structure of the SARS-CoV-2 spike S1 protein in complex with CR3022 Fab
分子名称: IgG H chain, IgG L chain, Spike glycoprotein
著者Huo, J, Zhao, Y, Ren, J, Zhou, D, Duyvesteyn, H.M.E, Carrique, L, Malinauskas, T, Ruza, R.R, Shah, P.N.M, Fry, E.E, Owens, R, Stuart, D.I.
登録日2020-04-15
公開日2020-04-29
最終更新日2022-04-06
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.
Cell Host Microbe, 28, 2020
6WKS
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BU of 6wks by Molmil
Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase, ADENOSINE, ...
著者Gupta, Y.K, Viswanathan, T, Arya, S, Qi, S, Misra, A, Chan, S.-H.
登録日2020-04-16
公開日2020-05-06
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structural basis of RNA cap modification by SARS-CoV-2.
Nat Commun, 11, 2020
6WOJ
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Structure of the SARS-CoV-2 macrodomain (NSP3) in complex with ADP-ribose
分子名称: ADENOSINE-5-DIPHOSPHORIBOSE, Non-structural protein 3
著者Lovell, S, Kashipathy, M.M, Battaile, K.P, Gao, F.P, Fehr, A.R.
登録日2020-04-24
公開日2020-05-06
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献The SARS-CoV-2 Conserved Macrodomain Is a Mono-ADP-Ribosylhydrolase.
J.Virol., 95, 2021
6WRH
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BU of 6wrh by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant
分子名称: CHLORIDE ION, GLYCEROL, Non-structural protein 3, ...
著者Osipiuk, J, Tesar, C, Jedrzejczak, R, Endres, M, Welk, L, Babnigg, G, Kim, Y, Michalska, K, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-04-29
公開日2020-05-06
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.
Nat Commun, 12, 2021
6YVA
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PLpro-C111S with mISG15
分子名称: Replicase polyprotein 1a, Ubiquitin-like protein ISG15, ZINC ION
著者Shin, D, Dikic, I.
登録日2020-04-28
公開日2020-05-13
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (3.18 Å)
主引用文献Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.
Nature, 587, 2020
6YYT
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BU of 6yyt by Molmil
Structure of replicating SARS-CoV-2 polymerase
分子名称: RNA product, ZINC ION, nsp12, ...
著者Hillen, H.S, Kokic, G, Farnung, L, Dienemann, C, Tegunov, D, Cramer, P.
登録日2020-05-06
公開日2020-05-13
最終更新日2020-08-19
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Structure of replicating SARS-CoV-2 polymerase.
Nature, 584, 2020
6YZ1
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BU of 6yz1 by Molmil
The crystal structure of SARS-CoV-2 nsp10-nsp16 methyltransferase complex with Sinefungin
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, SINEFUNGIN, ZINC ION, ...
著者Krafcikova, P, Silhan, J, Nencka, R, Boura, E.
登録日2020-05-06
公開日2020-05-13
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin.
Nat Commun, 11, 2020
7BZ5
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BU of 7bz5 by Molmil
Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of B38, Light chain of B38, ...
著者Wu, Y, Qi, J, Gao, F.
登録日2020-04-26
公開日2020-05-13
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.84 Å)
主引用文献A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2.
Science, 368, 2020
6WTT
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Crystals Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor GC-376
分子名称: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase, ...
著者Sacco, M, Ma, C, Chen, Y, Wang, J.
登録日2020-05-03
公開日2020-05-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.15 Å)
主引用文献Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease.
Cell Res., 30, 2020
6WUU
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Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250
分子名称: MAGNESIUM ION, Non-structural protein 3, VIR250, ...
著者Lv, Z, Olsen, S.K.
登録日2020-05-05
公開日2020-05-20
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.79 Å)
主引用文献Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design.
Sci Adv, 6, 2020
6WX4
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BU of 6wx4 by Molmil
Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR251
分子名称: Non-structural protein 3, VIR251, ZINC ION
著者Lv, Z, Olsen, S.K.
登録日2020-05-09
公開日2020-05-20
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (1.655 Å)
主引用文献Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design.
Sci Adv, 6, 2020
6WXD
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BU of 6wxd by Molmil
SARS-CoV-2 Nsp9 RNA-replicase
分子名称: Non-structural protein 9, SULFATE ION
著者Littler, D.R, Gully, B.S, Riboldi-Tunnicliffe, A, Rossjohn, J.
登録日2020-05-10
公開日2020-05-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9.
Iscience, 23, 2020
6WPS
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BU of 6wps by Molmil
Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment
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, S309 neutralizing antibody heavy chain, ...
著者Pinto, D, Park, Y.J, Beltramello, M, Walls, A.C, Tortorici, M.A, Bianchi, S, Jaconi, S, Culap, K, Zatta, F, De Marco, A, Peter, A, Guarino, B, Spreafico, R, Cameroni, E, Case, J.B, Chen, R.E, Havenar-Daughton, C, Snell, G, Virgin, H.W, Lanzavecchia, A, Diamond, M.S, Fink, K, Veesler, D, Corti, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2020-04-27
公開日2020-05-27
最終更新日2021-05-19
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody.
Nature, 583, 2020
6WZO
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BU of 6wzo by Molmil
Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form
分子名称: Nucleoprotein
著者Ye, Q, Corbett, K.D.
登録日2020-05-14
公開日2020-05-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.42 Å)
主引用文献Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
Protein Sci., 29, 2020
6WZQ
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BU of 6wzq by Molmil
Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P21 form
分子名称: Nucleoprotein, SULFATE ION
著者Ye, Q, Corbett, K.D.
登録日2020-05-14
公開日2020-05-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
Protein Sci., 29, 2020
6WZU
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BU of 6wzu by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group
分子名称: CHLORIDE ION, GLYCEROL, Non-structural protein 3, ...
著者Osipiuk, J, Tesar, C, Endres, M, Jedrzejczak, R, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-05-14
公開日2020-05-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.79 Å)
主引用文献Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.
Nat Commun, 12, 2021
6X1B
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BU of 6x1b by Molmil
Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.
分子名称: 1,2-ETHANEDIOL, DNA (5'-R(*GP*U)-3'), PHOSPHATE ION, ...
著者Kim, Y, Maltseva, N, Jedrzejczak, R, Welk, L, Endres, M, Chang, C, Michalska, K, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-05-18
公開日2020-05-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.97 Å)
主引用文献Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.
Commun Biol, 4, 2021
6X29
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BU of 6x29 by Molmil
SARS-CoV-2 rS2d Down State Spike Protein Trimer
分子名称: Spike glycoprotein
著者Henderson, R, Acharya, P.
登録日2020-05-20
公開日2020-05-27
最終更新日2020-10-21
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Controlling the SARS-CoV-2 spike glycoprotein conformation.
Nat.Struct.Mol.Biol., 27, 2020
6X2C
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SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer
分子名称: Spike glycoprotein
著者Henderson, R, Acharya, P.
登録日2020-05-20
公開日2020-05-27
最終更新日2021-07-07
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Controlling the SARS-CoV-2 spike glycoprotein conformation.
Nat.Struct.Mol.Biol., 27, 2020
7BW4
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Structure of the RNA-dependent RNA polymerase from SARS-CoV-2
分子名称: Non-structural protein 7, Non-structural protein 8, RNA-directed RNA polymerase, ...
著者Peng, Q, Peng, R, Shi, Y.
登録日2020-04-13
公開日2020-05-27
最終更新日2024-03-27
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2.
Cell Rep, 31, 2020

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