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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
9EWH
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BU of 9ewh by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Y109A
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-04-03
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.93 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9EXB
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BU of 9exb by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain NTD
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-04-06
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9EZB
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BU of 9ezb by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P67S
分子名称: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-04-11
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F5J
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BU of 9f5j by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Q58I
分子名称: CADMIUM ION, Nucleoprotein
著者Dhamotharan, K, Schlundt, A.
登録日2024-04-29
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F5L
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BU of 9f5l by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant A119S
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A.
登録日2024-04-29
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2.363 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F7A
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BU of 9f7a by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R
分子名称: Nucleoprotein, ZINC ION
著者Dhamotharan, K, Schlundt, A.
登録日2024-05-03
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F7C
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BU of 9f7c by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I
分子名称: Nucleoprotein, ZINC ION
著者Dhamotharan, K, Schlundt, A.
登録日2024-05-03
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F83
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BU of 9f83 by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant D63G
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-05-06
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9FBG
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BU of 9fbg by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P151S
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A.
登録日2024-05-13
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2.54 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
8RJ7
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BU of 8rj7 by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Camel-derived nanobody 1.29, LYSINE, ...
著者Casasnovas, J.M, Fernandez, L.A, Silva, K.
登録日2023-12-20
公開日2024-11-27
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
To Be Published
8YKN
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BU of 8ykn by Molmil
Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with X77
分子名称: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide, Non-structural protein 11
著者Wang, J, Zhang, J, Li, J.
登録日2024-03-05
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.77 Å)
主引用文献Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKP
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BU of 8ykp by Molmil
Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with X77
分子名称: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
著者Zou, X.F, Zhang, J, Li, J.
登録日2024-03-05
公開日2024-11-27
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
9CRC
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BU of 9crc by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 3 closed RBDs
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Ke, Z, Croll, T.I, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRE
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BU of 9cre by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 3 closed RBDs
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Ke, Z, Croll, T.I, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRG
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BU of 9crg by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Gamma (P.1) variant 3 closed RBDs
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Ke, Z, Kotecha, A, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRH
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BU of 9crh by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Delta (B.1.617.2) variant 3 closed RBDs
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Ke, Z, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRI
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BU of 9cri by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Mu (B.1.621) variant 3 closed RBDs
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Ke, Z, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
8R6E
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BU of 8r6e by Molmil
SARS-CoV-2 Nucleocapsid dimerization domain
分子名称: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLYCEROL, ...
著者Fahoum, J, Wiener, R, Rouvinski, A, Isupov, M.N.
登録日2023-11-22
公開日2024-12-04
実験手法X-RAY DIFFRACTION (1.53 Å)
主引用文献SARS-CoV-2 Nucleocapsid dimerization domain
To Be Published
8RNE
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BU of 8rne by Molmil
HLA-E*01:03 in complex with SARS-CoV-2 Nsp13 peptide, VMPLSAPTL
分子名称: Beta-2-microglobulin, HLA class I histocompatibility antigen, E alpha chain variant, ...
著者Sun, R, Achour, A, Sala, B.M, Sandalova, T.
登録日2024-01-09
公開日2024-12-04
最終更新日2025-01-22
実験手法X-RAY DIFFRACTION (1.71 Å)
主引用文献Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Plos Pathog., 20, 2024
8RNF
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BU of 8rnf by Molmil
HLA-E*01:03 in complex with SARS-CoV-2 Omicron Nsp13 peptide, VIPLSAPTL
分子名称: Beta-2-microglobulin, HLA class I histocompatibility antigen, E alpha chain variant, ...
著者Sun, R, Achour, A, Sala, B.M, Sandalova, T.
登録日2024-01-09
公開日2024-12-04
最終更新日2025-01-22
実験手法X-RAY DIFFRACTION (1.872 Å)
主引用文献Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Plos Pathog., 20, 2024
8USZ
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BU of 8usz by Molmil
Cryo-EM Structure of Full-Length Spike Protein of Omicron XBB.1.5
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Huynh, K.W, Chang, J.S, Fennell, K.F, Che, Y, Wu, H.
登録日2023-10-30
公開日2024-12-04
最終更新日2025-05-21
実験手法ELECTRON MICROSCOPY (2.98 Å)
主引用文献Preclinical characterization of the Omicron XBB.1.5-adapted BNT162b2 COVID-19 vaccine.
Npj Vaccines, 9, 2024
8XKO
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BU of 8xko by Molmil
CryoEM structure of compound HNC-1664 bound with RdRP-RNA complex of SARS-CoV-2
分子名称: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
著者Li, M, An, L, Hong, Y, Li, S, Zhang, K.
登録日2023-12-23
公開日2024-12-04
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.29 Å)
主引用文献An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode.
Nat Commun, 15, 2024
8YX5
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BU of 8yx5 by Molmil
Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-P35
分子名称: 5-[(1~{R},5~{S})-3,6-diazabicyclo[3.1.1]heptan-3-yl]-2-methyl-~{N}-[1-(1-methyl-2-oxidanylidene-benzo[cd]indol-6-yl)cyclopropyl]benzamide, GLYCEROL, Papain-like protease nsp3, ...
著者Lu, Y, Shang, J.
登録日2024-04-02
公開日2024-12-04
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19.
Nat Commun, 15, 2024
9B82
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BU of 9b82 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA2-15 antibody heavy chain, COVA2-15 antibody light chain, ...
著者Yuan, M, Zhu, X, Wilson, I.A.
登録日2024-03-28
公開日2024-12-04
最終更新日2025-01-08
実験手法X-RAY DIFFRACTION (3.38 Å)
主引用文献Plant-produced SARS-CoV-2 antibody engineered towards enhanced potency and in vivo efficacy.
Plant Biotechnol J, 23, 2025
8RBY
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BU of 8rby by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 3[N-MORPHOLINO]PROPANE SULFONIC ACID, Camel-derived nanobody 1.26, ...
著者Casasnovas, J.M, Fernandez, L.A, Silva, K.
登録日2023-12-05
公開日2024-12-11
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26
To Be Published

238582

件を2025-07-09に公開中

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