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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
7QNX
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The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with Beta-55 and EY6A Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-55 heavy chain, Beta-55 light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-12-23
公開日2022-01-19
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.92 Å)
主引用文献SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.
Cell, 185, 2022
7QNY
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The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with COVOX-58 and COVOX-158 Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVOX-158 heavy chain, COVOX-158 light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-12-23
公開日2022-01-19
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.84 Å)
主引用文献SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.
Cell, 185, 2022
7QO7
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SARS-CoV-2 S Omicron Spike B.1.1.529
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Ni, D, Lau, K, Turelli, P, Beckert, B, Nazarov, S, Pojer, F, Myasnikov, A, Stahlberg, H, Trono, D.
登録日2021-12-23
公開日2022-01-19
実験手法ELECTRON MICROSCOPY (3.02 Å)
主引用文献Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion
Biorxiv, 2021
7THH
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SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein
分子名称: 1,2-ETHANEDIOL, CHLORIDE ION, HEXAETHYLENE GLYCOL, ...
著者Osipiuk, J, Jedrzejczak, R, Endres, M, Wydorski, P, Joachimiak, L, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2022-01-11
公開日2022-01-19
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.32 Å)
主引用文献SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein
to be published
7VPH
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BU of 7vph by Molmil
Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98
分子名称: Isoform 3 of Nuclear pore complex protein Nup98-Nup96, ORF6 protein, mRNA export factor
著者Li, T, Guo, H, Yang, T, Wen, Y, Ji, X.
登録日2021-10-17
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export.
Front Mol Biosci, 8, 2021
7WBP
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Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with its receptor human 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, Angiotensin-converting enzyme 2, ...
著者Qi, J, Han, P.
登録日2021-12-17
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2.
Cell, 185, 2022
7WBQ
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Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike glycoprotein in complex with its receptor human 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, Angiotensin-converting enzyme 2, ...
著者Qi, J, Han, P.
登録日2021-12-17
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.34 Å)
主引用文献Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2.
Cell, 185, 2022
7EJL
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BU of 7ejl by Molmil
Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein
分子名称: 9-mer peptide from the HCoV spike protein, Beta-2-microglobulin, MHC class I antigen
著者Murayama, K, Kato-Murayama, M, Shirouzu, M.
登録日2021-04-02
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献Identification of TCR repertoires in functionally competent cytotoxic T cells cross-reactive to SARS-CoV-2.
Commun Biol, 4, 2021
7FCE
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Structure of the SARS-CoV-2 A372T spike glycoprotein (closed)
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Wang, X, Zhang, S.
登録日2021-07-14
公開日2022-01-26
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2.
Cell Res., 32, 2022
7OD3
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BU of 7od3 by Molmil
SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, LINOLEIC ACID, Spike glycoprotein
著者Toelzer, C, Gupta, K, Yadav, S.K.N, Borucu, U, Schaffitzel, C, Berger, I.
登録日2021-04-28
公開日2022-01-26
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2.
Nat Commun, 13, 2022
7TI9
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BU of 7ti9 by Molmil
Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2, form 2
分子名称: CHLORIDE ION, GLYCEROL, Papain-like protease nsp3
著者Stogios, P.J, Skarina, T, Di Leo, R, Savchenko, A, Joachimiak, A, Satchell, K.J.F, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2022-01-13
公開日2022-01-26
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.73 Å)
主引用文献Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2, form 2
To Be Published
7WK8
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BU of 7wk8 by Molmil
SARS-CoV-2 Omicron spike protein SD1 in complex with S3H3 Fab
分子名称: Heavy chain of S3H3 Fab, Light chain of S3H3 Fab, Spike glycoprotein
著者Hong, Q, Cong, Y.
登録日2022-01-08
公開日2022-01-26
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.61 Å)
主引用文献Molecular basis of receptor binding and antibody neutralization of Omicron.
Nature, 604, 2022
7F7E
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BU of 7f7e by Molmil
SARS-CoV-2 S protein RBD in complex with A5-10 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of A5-10 Fab, Light chain of A5-10 Fab, ...
著者Dou, Y, Wang, X, Wang, K, Liu, P, Lu, B.
登録日2021-06-29
公開日2022-02-02
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.49 Å)
主引用文献Etesevimab in combination with JS026 neutralizing SARS-CoV-2 and its variants.
Emerg Microbes Infect, 11, 2022
7NLL
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BU of 7nll by Molmil
SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody Fu2, Spike protein S1
著者Das, H, Hallberg, B.M.
登録日2021-02-22
公開日2022-02-02
最終更新日2023-09-27
実験手法ELECTRON MICROSCOPY (2.89 Å)
主引用文献A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo.
Nat Commun, 13, 2022
7NS6
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BU of 7ns6 by Molmil
SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fu2 nanobody, Spike glycoprotein,Fibritin, ...
著者Das, H, Hallberg, B.M.
登録日2021-03-05
公開日2022-02-02
実験手法ELECTRON MICROSCOPY (3.18 Å)
主引用文献A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo.
Nat Commun, 13, 2022
7NT4
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BU of 7nt4 by Molmil
X-ray structure of SCoV2-PLpro in complex with small molecule inhibitor
分子名称: 1,2-ETHANEDIOL, Non-structural protein 3, PROFLAVIN, ...
著者Napolitano, V, Mourao, A, Bostock, M, Matsuda, A, Czarna, A, Popowicz, G.M.
登録日2021-03-09
公開日2022-02-02
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.68 Å)
主引用文献Acriflavine, a clinically approved drug, inhibits SARS-CoV-2 and other betacoronaviruses.
Cell Chem Biol, 29, 2022
7PQY
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BU of 7pqy by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FI-3A Fab
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, FI-3A Fab heavy chain, FI-3A Fab light chain, ...
著者Zhou, D, Ren, J, Stuart, D.
登録日2021-09-20
公開日2022-02-02
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2.
Theranostics, 12, 2022
7PQZ
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BU of 7pqz by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FI-3A and FD-11A Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FD-11A Fab heavy chain, FD-11A Fab light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-09-20
公開日2022-02-02
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2.
Theranostics, 12, 2022
7PR0
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Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FD-5D Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, FD-5D Fab heavy chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-09-20
公開日2022-02-02
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.92 Å)
主引用文献Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2.
Theranostics, 12, 2022
7SC1
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BU of 7sc1 by Molmil
Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, R40-1G8
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, R40-1G8 Fab heavy chain, R40-1G8 Fab light chain, ...
著者Fan, C, Bjorkman, P.J.
登録日2021-09-26
公開日2022-02-02
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers.
Cell Host Microbe, 30, 2022
7TLB
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BU of 7tlb by Molmil
Down-state locked rS2d SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 2
分子名称: Spike glycoprotein
著者Henderson, R, Acharya, P.
登録日2022-01-18
公開日2022-02-02
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.06 Å)
主引用文献Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82, 2022
7TLC
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BU of 7tlc by Molmil
Down-state locked, S2 stabilized rS2d-HexaPro SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 1
分子名称: Spike glycoprotein
著者Henderson, R, Acharya, P.
登録日2022-01-18
公開日2022-02-02
最終更新日2023-04-12
実験手法ELECTRON MICROSCOPY (2.83 Å)
主引用文献Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82, 2022
7TLY
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BU of 7tly by Molmil
SARS-CoV-2 S B.1.1.529 Omicron variant (RBD + S309 Local Refinement)
分子名称: S309 Fab heavy chain, S309 Fab light chain, Spike glycoprotein, ...
著者McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2022-01-19
公開日2022-02-02
最終更新日2022-03-09
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement.
Science, 375, 2022
7TM0
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BU of 7tm0 by Molmil
SARS-CoV-2 S B.1.1.529 Omicron variant + S309 + S2L20 Global Refinement
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, S2L20 Fab heavy chain, ...
著者McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2022-01-19
公開日2022-02-02
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement.
Science, 375, 2022
7TN0
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SARS-CoV-2 Omicron RBD in complex with human ACE2 and S304 Fab and S309 Fab
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, ...
著者McCallum, M, Czudnochowski, N, Nix, J.C, Croll, T.I, SSGCID, Dillen, J.R, Snell, G, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2022-01-20
公開日2022-02-02
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.85 Å)
主引用文献Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement.
Science, 375, 2022

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