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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
8HG0
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BU of 8hg0 by Molmil
Cryo-EM structure of SARS-CoV-2 prototype spike protein receptor-binding domain in complex with white-tailed deer ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
著者Han, P, Meng, Y.M, Qi, J.X.
登録日2022-11-13
公開日2023-08-30
最終更新日2023-10-25
実験手法ELECTRON MICROSCOPY (3.51 Å)
主引用文献Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity.
J.Virol., 97, 2023
8HTV
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BU of 8htv by Molmil
SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3a
分子名称: 1-(5,6-dihydrobenzo[b][1]benzazepin-11-yl)-2-sulfanyl-ethanone, 3C-like proteinase
著者Su, H.X, Nie, T.Q, Li, M.J, Xu, Y.C.
登録日2022-12-21
公開日2023-08-30
最終更新日2023-09-27
実験手法X-RAY DIFFRACTION (2.04 Å)
主引用文献Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group.
J.Med.Chem., 66, 2023
8IFY
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BU of 8ify by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer 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, ...
著者Han, P, Meng, Y.M, Qi, J.X.
登録日2023-02-20
公開日2023-08-30
最終更新日2023-10-25
実験手法ELECTRON MICROSCOPY (2.55 Å)
主引用文献Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity.
J.Virol., 97, 2023
8IFZ
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BU of 8ifz by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein receptor-binding domain in complex with white-tailed deer ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
著者Han, P, Meng, Y.M, Qi, J.X.
登録日2023-02-20
公開日2023-08-30
最終更新日2023-10-25
実験手法ELECTRON MICROSCOPY (2.85 Å)
主引用文献Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity.
J.Virol., 97, 2023
8STY
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BU of 8sty by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI60
分子名称: 3C-like proteinase nsp5, benzyl (3S)-3-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-2-azaspiro[4.4]nonane-2-carboxylate
著者Blankenship, L.B, Liu, W.R.
登録日2023-05-11
公開日2023-08-30
最終更新日2024-05-01
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 66, 2023
8STZ
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BU of 8stz by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI37
分子名称: 3C-like proteinase nsp5, benzyl (3S)-3-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-2-azaspiro[4.5]decane-2-carboxylate
著者Blankenship, L.B, Liu, W.R.
登録日2023-05-11
公開日2023-08-30
最終更新日2024-05-01
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 66, 2023
8SXR
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Crystal structure of SARS-CoV-2 Mpro with C5a
分子名称: 3C-like proteinase nsp5, N-[(4-chlorothiophen-2-yl)methyl]-N-[4-(dimethylamino)phenyl]-2-(5-hydroxyisoquinolin-4-yl)acetamide
著者Worrall, L.J, Kenward, C, Lee, J, Strynadka, N.C.J.
登録日2023-05-23
公開日2023-08-30
実験手法X-RAY DIFFRACTION (2.114 Å)
主引用文献A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants.
Emerg Microbes Infect, 12, 2023
7U92
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SARS-CoV-2 Main Protease (Mpro) in Complex with ML1006a
分子名称: (1R,2S,5S)-N-{(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase, CHLORIDE ION
著者Westberg, M, Fernandez, D, Lin, M.Z.
登録日2022-03-09
公開日2023-09-06
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations.
Sci Transl Med, 16, 2024
7Y0O
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BU of 7y0o by Molmil
Interface of SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody
分子名称: P14 nanobody, Spike protein S1, heavy chain of R15, ...
著者Wang, L.
登録日2022-06-05
公開日2023-09-06
実験手法ELECTRON MICROSCOPY (4.4 Å)
主引用文献SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody
To Be Published
7YBK
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BU of 7ybk by Molmil
SARS-CoV-2 B.1.620 variant spike (open 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Wang, X, Fu, W.
登録日2022-06-29
公開日2023-09-06
最終更新日2024-03-20
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants.
Virol Sin, 37, 2022
7YLB
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BU of 7ylb by Molmil
Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis
分子名称: NC2, Nucleoprotein, SULFATE ION
著者Hu, M, Du, Y, Sun, R, Hao, Q.
登録日2022-07-26
公開日2023-09-06
実験手法X-RAY DIFFRACTION (2.41 Å)
主引用文献Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis
To Be Published
8GSB
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BU of 8gsb by Molmil
SARS-COV-2 BA.1 Spike incomplex with VacBB-665
分子名称: Light chain of VacBB-665, Spike protein S1, heavy chain of VacBB-665
著者Liu, C.C, Ju, B, Shen, S.L, Zhang, Z.
登録日2022-09-05
公開日2023-09-06
実験手法ELECTRON MICROSCOPY (3.99 Å)
主引用文献Complex of SARS-COV-2 spike BA.1 and VacBB-665
To Be Published
7XY3
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BU of 7xy3 by Molmil
Cryo-EM structure of SARS-CoV-2 spike in complex with VHH14
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, VHH14
著者Cao, D, Fan, X, Zhang, X.
登録日2022-05-31
公開日2023-09-13
実験手法ELECTRON MICROSCOPY (4.6 Å)
主引用文献Identification of nano-abzymes to catalyze the spike-trimer of SARS-CoV-2
To Be Published
7XY4
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BU of 7xy4 by Molmil
Cryo-EM structure of SARS-CoV-2 spike in complex with VHH21
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, VHH21
著者Cao, D, Fan, X, Zhang, X.
登録日2022-05-31
公開日2023-09-13
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Identification of nano-abzymes to catalyze the spike-trimer of SARS-CoV-2
To Be Published
7Y0N
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BU of 7y0n by Molmil
SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody
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, Heavy chain of R15-F7, ...
著者Wang, L.
登録日2022-06-05
公開日2023-09-13
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody
To Be Published
8AZC
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BU of 8azc by Molmil
Structure of SARS-CoV-2 NSP3 macrodomain in the apo form
分子名称: 3[N-MORPHOLINO]PROPANE SULFONIC ACID, CHLORIDE ION, Papain-like protease nsp3
著者Sander, S, Tidow, H, Fliegert, R, Sandmann, M.
登録日2022-09-05
公開日2023-09-13
実験手法X-RAY DIFFRACTION (0.93 Å)
主引用文献Structure of SARS-CoV-2 NSP3 macrodomain in the apo form
To Be Published
8AZD
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BU of 8azd by Molmil
Structure of SARS-CoV-2 NSP3 macrodomain in complex with ADPR
分子名称: ADENOSINE-5-DIPHOSPHORIBOSE, Papain-like protease nsp3
著者Sander, S, Tidow, H, Fliegert, R, Sandmann, M.
登録日2022-09-05
公開日2023-09-13
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Structure of SARS-CoV-2 NSP3 macrodomain in the apo form
To Be Published
8F0I
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BU of 8f0i by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody COVA309-22
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA309-22 heavy chain, COVA309-22 light chain, ...
著者Yuan, M, Wilson, I.A.
登録日2022-11-03
公開日2023-09-13
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (3.7 Å)
主引用文献Broad SARS-CoV-2 neutralization by monoclonal and bispecific antibodies derived from a Gamma-infected individual.
Iscience, 26, 2023
8GTV
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BU of 8gtv by Molmil
SARS-CoV-2 3CL protease (3CLpro) in complex with compound JZD-07
分子名称: 3C-like proteinase, 4-[(2~{S})-4-(3,4-dichlorophenyl)-2-(morpholin-4-ylmethyl)piperazin-1-yl]carbonyl-1~{H}-quinolin-2-one
著者Su, H.X, Nie, T.Q, Xie, H, Li, M.J, Xu, Y.C.
登録日2022-09-08
公開日2023-09-13
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Development of novel inhibitors against SARS-CoV-2 3CLpro
To Be Published
8GTW
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BU of 8gtw by Molmil
SARS-CoV-2 3CL protease (3CLpro) in complex with compound JZD-26
分子名称: (2S)-4-(3,4-dichlorophenyl)-1-[(2-oxidanylidene-1H-quinolin-4-yl)carbonyl]-N-[3,3,3-tris(fluoranyl)propyl]piperazine-2-carboxamide, 3C-like proteinase
著者Su, H.X, Nie, T.Q, Xie, H, Li, M.J, Xu, Y.C.
登録日2022-09-08
公開日2023-09-13
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Development of novel inhibitors against SARS-CoV-2 3CLpro
To Be Published
8U2X
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BU of 8u2x by Molmil
Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2 (H235A mutant)
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, Uridylate-specific endoribonuclease nsp15
著者Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2023-09-06
公開日2023-09-13
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2 (H235A mutant)
To be published
7YR4
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BU of 7yr4 by Molmil
SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(interface)
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Wang, L.
登録日2022-08-08
公開日2023-09-20
実験手法ELECTRON MICROSCOPY (4.12 Å)
主引用文献BA.2.75 in complex with ACE2
To Be Published
8CQ1
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BU of 8cq1 by Molmil
Stem-Loop 4 of the 5'-UTR of the SARS-CoV2 genomic RNA
分子名称: 5_SL4
著者Duchardt-Ferner, E, Voegele, J.
登録日2023-03-03
公開日2023-09-20
最終更新日2023-11-22
実験手法SOLUTION NMR
主引用文献High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.
Nucleic Acids Res., 51, 2023
8EDF
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BU of 8edf by Molmil
Bovine Fab SKD in complex with Sars COV-2 receptor binding domain
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, SKD Fab Light chain, SKD Fab heavy chain, ...
著者Stanfield, R.L, Wilson, I.A.
登録日2022-09-04
公開日2023-09-20
最終更新日2023-10-04
実験手法X-RAY DIFFRACTION (3.4 Å)
主引用文献The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
8GVD
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BU of 8gvd by Molmil
SARS-CoV-2 Mpro in complex with D-4-38
分子名称: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE, 3C-like proteinase nsp5
著者Liu, M, Huang, H.
登録日2022-09-14
公開日2023-09-20
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献SARS-CoV-2 Mpro in complex with D-4-38
To Be Published

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件を2024-07-10に公開中

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