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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
9C2H
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BU of 9c2h by Molmil
SARS-CoV-2 Nucleocapsid Dimerization Domain bound to Fab-NP1E9 and Fab-NP3B4
分子名称: Antibody Fab NP1-E9 Heavy Chain (variable region), Antibody Fab NP1-E9 Light Chain (variable region), Antibody Fab NP3-B4 Heavy Chain (variable region), ...
著者Landeras-Bueno, S, Hariharan, C, Diaz Avalos, R, Ollmann Saphire, E.
登録日2024-05-31
公開日2025-05-14
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome
To Be Published
9F7P
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BU of 9f7p by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S mutant
分子名称: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, MALONATE ION, ...
著者Camara-Artigas, A.
登録日2024-05-04
公開日2025-05-14
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献SARS-CoV-2 papain-like protease (PLpro) C112S mutant
To Be Published
9F7R
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BU of 9f7r by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S mutant
分子名称: GLYCEROL, PHOSPHATE ION, Replicase polyprotein 1ab, ...
著者Camara-Artigas, A.
登録日2024-05-04
公開日2025-05-14
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献SARS-CoV-2 papain-like protease (PLpro) C112S mutant
To Be Published
9F7S
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BU of 9f7s by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-K229R mutant
分子名称: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, MALONATE ION, ...
著者Camara-Artigas, A.
登録日2024-05-04
公開日2025-05-14
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-K229R mutant
To Be Published
9F7U
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BU of 9f7u by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-Q222D-K229R-Q230R-C271S mutant
分子名称: CHLORIDE ION, GLYCEROL, MALONIC ACID, ...
著者Camara-Artigas, A.
登録日2024-05-05
公開日2025-05-14
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-Q222D-K229R-Q230R-C271S mutant
To Be Published
9LVR
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BU of 9lvr by Molmil
Crystal structure of SARS-CoV-2 3CL protease in complex with compound 1
分子名称: 1,2-ETHANEDIOL, 3C-like proteinase nsp5, 6-(1,3-dihydroisoindol-2-yl)-3-(5-methylpyridin-3-yl)-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
著者Unoh, Y, Hirai, K, Uehara, S, Kawashima, S, Nobori, H, Sato, J, Shibayama, H, Hori, A, Nakahara, K, Kurahashi, K, Takamatsu, M, Yamamoto, S, Zhang, O, Tanimura, M, Dodo, R, Maruyama, Y, Sawa, H, Watari, R, Miyano, T, Kato, T, Sato, T, Tachibana, Y.
登録日2025-02-12
公開日2025-05-14
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Discovery of The Clinical Candidate S-892216: A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19
To Be Published
9FCM
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BU of 9fcm by Molmil
Single-domain antibody binding the SARS-COV2 S2
分子名称: CHLORIDE ION, Single-domain antibody R3DC23, Spike protein S2'
著者Vann Molle, I, Remaut, H.
登録日2024-05-15
公開日2025-05-21
最終更新日2025-06-11
実験手法X-RAY DIFFRACTION (1.94 Å)
主引用文献Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that clamp the spike at its base.
Nat Commun, 16, 2025
9UJ2
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BU of 9uj2 by Molmil
14-3-3 zeta chimera with the S202R peptide of SARS-CoV-2 N (residues 200-213)
分子名称: 1,2-ETHANEDIOL, 14-3-3 protein zeta/delta,Peptide from Nucleoprotein, DI(HYDROXYETHYL)ETHER
著者Boyko, K.M, Matyuta, I.O, Minyaev, M.E, Perfilova, K.V, Sluchanko, N.N.
登録日2025-04-16
公開日2025-05-21
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness.
Biochem.Biophys.Res.Commun., 767, 2025
9ELE
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BU of 9ele by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 RBD in complex with human ACE2 (local refinement of RBD and hACE2)
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, Processed angiotensin-converting enzyme 2, ...
著者Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-05-28
実験手法ELECTRON MICROSCOPY (3.16 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELF
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BU of 9elf by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with 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, Processed angiotensin-converting enzyme 2, ...
著者Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-05-28
実験手法ELECTRON MICROSCOPY (2.88 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELG
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BU of 9elg by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike RBD and NTD (local refinement of RBD and NTD)
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 protein S1
著者Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-05-28
実験手法ELECTRON MICROSCOPY (3.71 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELH
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BU of 9elh by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (one RBD up 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Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-05-28
実験手法ELECTRON MICROSCOPY (2.98 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELI
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BU of 9eli by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (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Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-05-28
実験手法ELECTRON MICROSCOPY (2.82 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELO
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BU of 9elo by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+S31 deletion spike protein (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Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-05-28
実験手法ELECTRON MICROSCOPY (2.74 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELQ
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BU of 9elq by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11.1+S31 deletion spike protein (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Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-05-28
実験手法ELECTRON MICROSCOPY (2.64 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9HH5
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BU of 9hh5 by Molmil
Crystal Structure of nsp15 Endoribonuclease from SARS CoV-2 in Complex with Sepantronium (YM-155)
分子名称: 1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl)benzo[f]benzimidazol-3-ium-4,9-dione, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Nsp15 - Uridylate-specific endoribonuclease, ...
著者Chatziefthymiou, S.D, Kolbe, M, Hakanpaeae, J, Labahn, J, Windshuegel, B.
登録日2024-11-21
公開日2025-05-28
実験手法X-RAY DIFFRACTION (2.08 Å)
主引用文献Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15.
Protein Sci., 34, 2025
9HH6
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BU of 9hh6 by Molmil
Crystal Structure of Nsp15 Endoribonuclease from SARS CoV-2 in Complex with TAS-103
分子名称: 1,2-ETHANEDIOL, 6-[2-(dimethylamino)ethylamino]-3-oxidanyl-indeno[2,1-c]quinolin-7-one, ORF1ab polyprotein, ...
著者Chatziefthymiou, S.D, Kolbe, M, Hakanpaeae, J, Labahn, J, Windshuegel, B.
登録日2024-11-21
公開日2025-05-28
実験手法SOLUTION SCATTERING (2 Å), X-RAY DIFFRACTION
主引用文献Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15.
Protein Sci., 34, 2025
9IZB
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BU of 9izb by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with TMP1
分子名称: 3C-like proteinase nsp5, TMP1
著者Deng, X.Y, Zeng, R, Yang, S.Y, Lei, J.
登録日2024-08-01
公開日2025-05-28
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Crystal structure of SARS-CoV-2 main protease in complex with TMP1
To Be Published
9ELK
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BU of 9elk by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (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Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-06-04
実験手法ELECTRON MICROSCOPY (2.82 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELL
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BU of 9ell by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (one RBD up 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Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-06-04
実験手法ELECTRON MICROSCOPY (2.93 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELM
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BU of 9elm by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (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Feng, Z, Huang, J, Ward, A.B.
登録日2024-12-04
公開日2025-06-04
実験手法ELECTRON MICROSCOPY (2.68 Å)
主引用文献Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ML4
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BU of 9ml4 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-A10 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-A10 heavy chain, M8b-A10 light chain, ...
著者Fan, C, Bjorkman, P.J.
登録日2024-12-18
公開日2025-06-04
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML5
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BU of 9ml5 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-B8 Fab
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, M8b-B8 heavy chain, ...
著者Fan, C, Bjorkman, P.J.
登録日2024-12-18
公開日2025-06-04
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML6
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BU of 9ml6 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C9 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-C9 heavy chain, M8b-C9 light chain, ...
著者Fan, C, Bjorkman, P.J.
登録日2024-12-18
公開日2025-06-04
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML7
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BU of 9ml7 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C10 Fab
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, M8b-C10 heavy chain, ...
著者Fan, C, Bjorkman, P.J.
登録日2024-12-18
公開日2025-06-04
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025

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件を2025-07-09に公開中

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