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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
6ZP1
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BU of 6zp1 by Molmil
Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Closed State
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Xiong, X, Qu, K, Scheres, S.H.W, Briggs, J.A.G.
登録日2020-07-08
公開日2020-07-22
最終更新日2021-06-02
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献A thermostable, closed SARS-CoV-2 spike protein trimer.
Nat.Struct.Mol.Biol., 27, 2020
6ZP2
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BU of 6zp2 by Molmil
Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Locked State
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, BILIVERDINE IX ALPHA, ...
著者Xiong, X, Qu, K, Scheres, S.H.W, Briggs, J.A.G.
登録日2020-07-08
公開日2020-07-22
最終更新日2022-03-02
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献A thermostable, closed SARS-CoV-2 spike protein trimer.
Nat.Struct.Mol.Biol., 27, 2020
6XQB
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BU of 6xqb by Molmil
SARS-CoV-2 RdRp/RNA complex
分子名称: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
著者Liu, B, Shi, W, Yang, Y.
登録日2020-07-09
公開日2020-07-29
最終更新日2024-03-06
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Structure of SARS-CoV-2 RdRp/RNA complex at 3.4 Angstroms resolution
To Be Published
6ZBP
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BU of 6zbp by Molmil
H11-H4 complex with SARS-CoV-2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, H11-H4, SULFATE ION, ...
著者Naismith, J.H, Huo, J, Mikolajek, H, Ward, P, Dumoux, M, Owens, R.J, LeBas, A.
登録日2020-06-08
公開日2020-07-29
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献H11-D4 complex with SARS-CoV-2 RBD
To Be Published
6ZHD
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BU of 6zhd by Molmil
H11-H4 bound to Spike
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, Nanobody H11-H4, ...
著者Clare, D.K, Naismith, J.H, Weckener, M, Vogirala, V.K.
登録日2020-06-22
公開日2020-07-29
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献H11-H4 bound to Spike
To Be Published
6ZLW
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BU of 6zlw by Molmil
SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-01
公開日2020-07-29
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZM7
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BU of 6zm7 by Molmil
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex
分子名称: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-01
公開日2020-07-29
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZN5
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BU of 6zn5 by Molmil
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-06
公開日2020-07-29
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZOK
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BU of 6zok by Molmil
SARS-CoV-2-Nsp1-40S complex, focused on body
分子名称: 18S ribosomal RNA, 40S ribosomal protein S11, 40S ribosomal protein S13, ...
著者Schubert, K, Karousis, E.D, Jomaa, A, Scaiola, A, Echeverria, B, Gurzeler, L.-A, Leibundgut, M, Thiel, V, Muehlemann, O, Ban, N.
登録日2020-07-07
公開日2020-07-29
最終更新日2021-02-10
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
Nat.Struct.Mol.Biol., 27, 2020
6ZON
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BU of 6zon by Molmil
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-07
公開日2020-07-29
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZOW
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BU of 6zow by Molmil
SARS-CoV-2 spike in prefusion state
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, DIMETHYL SULFOXIDE, ...
著者Martinez, M, Marabini, R, Carazo, J.M.
登録日2020-07-07
公開日2020-07-29
最終更新日2022-12-21
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.
Iucrj, 7, 2020
6ZP4
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BU of 6zp4 by Molmil
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-08
公開日2020-07-29
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZSL
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BU of 6zsl by Molmil
Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution
分子名称: PHOSPHATE ION, SARS-CoV-2 helicase NSP13, ZINC ION
著者Newman, J.A, Yosaatmadja, Y, Douangamath, A, Arrowsmith, C.H, von Delft, F, Edwards, A, Bountra, C, Gileadi, O.
登録日2020-07-15
公開日2020-07-29
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.94 Å)
主引用文献Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Nat Commun, 12, 2021
6XLU
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BU of 6xlu by Molmil
Structure of SARS-CoV-2 spike at pH 4.0
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Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
登録日2020-06-29
公開日2020-08-12
最終更新日2021-12-15
実験手法ELECTRON MICROSCOPY (2.4 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
6ZME
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BU of 6zme by Molmil
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex
分子名称: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-02
公開日2020-08-12
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
7CAH
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BU of 7cah by Molmil
The interface of H014 Fab binds to SARS-CoV-2 S
分子名称: Heavy chain of H014 Fab, Light chain of H014 Fab, Spike protein S1
著者Zhe, L, Cao, L, Deng, Y, Sun, Y, Wang, N, Xie, L, Rao, Z, wang, Y, Qin, C, Wang, X.
登録日2020-06-08
公開日2020-08-12
最終更新日2021-03-10
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody.
Science, 369, 2020
6X79
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BU of 6x79 by Molmil
Prefusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed 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McCallum, M, Walls, A.C, Corti, D, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2020-05-29
公開日2020-08-19
最終更新日2021-01-27
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation.
Nat.Struct.Mol.Biol., 27, 2020
6XRZ
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BU of 6xrz by Molmil
The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome
分子名称: Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome
著者Zhang, K, Zheludev, I, Hagey, R, Wu, M, Haslecker, R, Hou, Y, Kretsch, R, Pintilie, G, Rangan, R, Kladwang, W, Li, S, Pham, E, Souibgui, C, Baric, R, Sheahan, T, Souza, V, Glenn, J, Chiu, W, Das, R.
登録日2020-07-14
公開日2020-08-19
最終更新日2024-03-06
実験手法ELECTRON MICROSCOPY (6.9 Å)
主引用文献Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome.
Biorxiv, 2020
6ZMI
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BU of 6zmi by Molmil
SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex
分子名称: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-02
公開日2020-08-19
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZMO
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BU of 6zmo by Molmil
SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex
分子名称: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-03
公開日2020-08-19
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZMT
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BU of 6zmt by Molmil
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-03
公開日2020-08-19
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6W79
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BU of 6w79 by Molmil
Structure of SARS-CoV main protease bound to potent broad-spectrum non-covalent inhibitor X77
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, DIMETHYL SULFOXIDE, Main protease, ...
著者Mesecar, A.D, StJohn, S, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-03-18
公開日2020-08-26
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.46 Å)
主引用文献A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19)
To Be Published
7CN9
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BU of 7cn9 by Molmil
Cryo-EM structure of SARS-CoV-2 Spike ectodomain
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Ho, M, Chang, Y, Wang, C, Wu, Y, Huang, H, Chen, T, Lo, J.M, Chen, X, Ma, C.
登録日2020-07-30
公開日2020-08-26
最終更新日2021-03-10
実験手法ELECTRON MICROSCOPY (4.7 Å)
主引用文献A Carbohydrate-Binding Protein from the Edible Lablab Beans Effectively Blocks the Infections of Influenza Viruses and SARS-CoV-2.
Cell Rep, 32, 2020
7JJI
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BU of 7jji by Molmil
Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
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-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside, ...
著者Bangaru, S, Turner, H.L, Ozorowski, G, Antanasijevic, A, Ward, A.B.
登録日2020-07-26
公開日2020-08-26
最終更新日2020-12-23
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate.
Science, 370, 2020
7JLT
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BU of 7jlt by Molmil
Crystal Structure of SARS-CoV-2 NSP7-NSP8 complex.
分子名称: Non-structural protein 7, Non-structural protein 8
著者Biswal, M, Hai, R, Song, J.
登録日2020-07-30
公開日2020-08-26
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Two conserved oligomer interfaces of NSP7 and NSP8 underpin the dynamic assembly of SARS-CoV-2 RdRP.
Nucleic Acids Res., 49, 2021

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