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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
9AUK
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BU of 9auk by Molmil
Structure of SARS-CoV-2 Mpro mutant (A173V) in complex with Nirmatrelvir (PF-07321332)
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Gajiwala, K.S, Greasley, S.E, Ferre, R.A, Liu, W, Stewart, A.E.
登録日2024-02-29
公開日2024-08-07
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance.
Sci Adv, 10, 2024
9AUL
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BU of 9aul by Molmil
Structure of SARS-CoV-2 Mpro mutant (A173V,T304I)) in complex with Nirmatrelvir (PF-07321332)
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Gajiwala, K.S, Greasley, S.E, Ferre, R.A, Liu, W, Stewart, A.E.
登録日2024-02-29
公開日2024-08-07
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.421 Å)
主引用文献In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance.
Sci Adv, 10, 2024
9AUM
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BU of 9aum by Molmil
Structure of SARS-CoV-2 Mpro mutant (T21I,S144A,T304I) in complex with Nirmatrelvir (PF-07321332)
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Gajiwala, K.S, Greasley, S.E, Ferre, R.A, Liu, W, Stewart, A.E.
登録日2024-02-29
公開日2024-08-07
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.539 Å)
主引用文献In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance.
Sci Adv, 10, 2024
9AUN
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BU of 9aun by Molmil
Structure of SARS-CoV-2 Mpro mutant (T21I,T304I)
分子名称: 3C-like proteinase nsp5
著者Gajiwala, K.S, Greasley, S.E, Ferre, R.A, Liu, W, Stewart, A.E.
登録日2024-02-29
公開日2024-08-07
実験手法X-RAY DIFFRACTION (2.29 Å)
主引用文献In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance.
Sci Adv, 10, 2024
9AUO
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BU of 9auo by Molmil
Structure of SARS-CoV-2 Mpro mutant (L50F,T304I)
分子名称: 3C-like proteinase nsp5
著者Gajiwala, K.S, Greasley, S.E, Ferre, R.A, Liu, W, Stewart, A.E.
登録日2024-02-29
公開日2024-08-07
実験手法X-RAY DIFFRACTION (2.423 Å)
主引用文献In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance.
Sci Adv, 10, 2024
9BPF
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BU of 9bpf by Molmil
Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor
分子名称: 3C-like proteinase nsp5, N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide
著者Chen, P, Arutyunova, E, Lemieux, M.J.
登録日2024-05-07
公開日2024-08-07
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献A Structural Comparison of Oral SARS-CoV-2 Drug Candidate Ibuzatrelvir Complexed with the Main Protease (M pro ) of SARS-CoV-2 and MERS-CoV.
Jacs Au, 4, 2024
8KDM
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BU of 8kdm by Molmil
Structure of SARS-CoV Spike protein complexed with antibody PW5-5
分子名称: PW5-5 heavy chain, PW5-5 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-09
公開日2024-08-14
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (2.87 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KDR
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BU of 8kdr by Molmil
The local refined map of SARS-CoV-2 XBB Variant Spike protein complexed with antibody PW5-535
分子名称: PW5-535 heavy chain, PW5-535 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-10
公開日2024-08-14
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KDS
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BU of 8kds by Molmil
Trimer state of SARS-CoV Spike protein complexed with antibody PW5-535
分子名称: PW5-535 heavy chain, PW5-535 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-10
公開日2024-08-14
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.05 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KDT
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BU of 8kdt by Molmil
The local refined map of SARS-CoV Spike protein complexed with antibody PW5-5
分子名称: PW5-5 heavy chain, PW5-5 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-10
公開日2024-08-14
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.04 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KEJ
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BU of 8kej by Molmil
Monomer state of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5
分子名称: PW5-5 heavy chain, PW5-5 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-11
公開日2024-08-14
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.73 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KEK
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BU of 8kek by Molmil
Monomer state of SARS-CoV Spike protein complexed with antibody PW5-535
分子名称: PW5-535 heavy chain, PW5-535 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-11
公開日2024-08-14
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.54 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KEO
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BU of 8keo by Molmil
Structure of SARS-CoV-2 Omicron BA.1 Spike complexed with antibody PW5-570
分子名称: PW5-570 heavy chain, PW5-570 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-13
公開日2024-08-14
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.78 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KEP
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BU of 8kep by Molmil
The local refined map of SARS-CoV-2 Omicron BA.1 Spike complexed with antibody PW5-570
分子名称: PW5-570 heavy chain, PW5-570 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-13
公開日2024-08-14
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (2.93 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KEQ
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BU of 8keq by Molmil
State 1 of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5
分子名称: PW5-5 heavy chain, PW5-5 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-13
公開日2024-08-14
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.14 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8KER
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BU of 8ker by Molmil
Structure of SARS-CoV-2 XBB Variant Spike protein complexed with broadly neutralizing antibody PW5-535
分子名称: PW5-535 heavy chain, PW5-535 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-13
公開日2024-08-14
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.95 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8TQH
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BU of 8tqh by Molmil
MPI68 bound to Mpro of SARS-CoV-2
分子名称: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-L-leucinamide
著者Blankenship, L.R, Liu, W.R.
登録日2023-08-07
公開日2024-08-14
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献MPI68 bound to SARS-CoV-2 Mpro
To Be Published
8TQJ
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BU of 8tqj by Molmil
MPI57 bound to Mpro of SARS-CoV-2
分子名称: 3C-like proteinase nsp5, benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate
著者Blankenship, L.R, Liu, W.R.
登録日2023-08-07
公開日2024-08-14
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献MPI57 bound to SARS-CoV-2 Mpro
To Be Published
8TQL
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BU of 8tql by Molmil
MPI54 bound to Mpro of SARS-CoV-2
分子名称: 3C-like proteinase nsp5, benzyl [(2S,3S)-3-tert-butoxy-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxobutan-2-yl]carbamate
著者Blankenship, L.R, Liu, W.R.
登録日2023-08-07
公開日2024-08-14
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献MPI54 bound to SARS-CoV-2 Mpro
To Be Published
8TQT
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BU of 8tqt by Molmil
MPI52 bound to Mpro of SARS-CoV-2
分子名称: (3-chlorophenyl)methyl [(2S)-3-cyclohexyl-1-({(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}amino)-1-oxopropan-2-yl]carbamate, 3C-like proteinase nsp5
著者Blankenship, L.R, Liu, W.R.
登録日2023-08-08
公開日2024-08-14
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献MPI52 bound to SARS-CoV-2 Mpro
To Be Published
8TQU
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BU of 8tqu by Molmil
MPI51 bound to Mpro of SARS-CoV-2
分子名称: 3C-like proteinase nsp5, UAW247
著者Blankenship, L.R, Liu, W.R.
登録日2023-08-08
公開日2024-08-14
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献MPI51 bound to SARS-CoV-2 Mpro
To Be Published
8VDJ
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BU of 8vdj by Molmil
Crystal structure of SARS-CoV-2 3CL protease (3CLpro) as a covalent complex with EDP-235
分子名称: 3C-like proteinase nsp5, 4,6,7-trifluoro-N-{(2S)-1-[(3R,5'R)-5'-(iminomethyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidin]-1'-yl]-4-methyl-1-oxopentan-2-yl}-N-methyl-1H-indole-2-carboxamide, THIOCYANATE ION
著者Cade, I.A, Rhodin, M.H.J.
登録日2023-12-15
公開日2024-08-14
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.002 Å)
主引用文献The small molecule inhibitor of SARS-CoV-2 3CLpro EDP-235 prevents viral replication and transmission in vivo.
Nat Commun, 15, 2024
9FJK
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BU of 9fjk by Molmil
Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6
分子名称: K501SP6 Fv Heavy Chain, K501SP6 Fv Light Chain, Spike glycoprotein,Fibritin
著者Bjoernsson, K.H, Walker, M.R, Raghavan, S.S.R, Ward, A.B, Barfod, L.K.
登録日2024-05-31
公開日2024-08-14
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.84 Å)
主引用文献Broadly potent spike-specific human monoclonal antibodies inhibit SARS-CoV-2 Omicron sub-lineages.
Commun Biol, 7, 2024
8UPX
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BU of 8upx by Molmil
Omicron-S-MERS-RBD
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,SARS-CoV-2 omicron spike with MERS RBD
著者Bu, F, Li, F, Liu, B.
登録日2023-10-23
公開日2024-08-21
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Pan-beta-coronavirus subunit vaccine prevents SARS-CoV-2 Omicron, SARS-CoV, and MERS-CoV challenge.
J.Virol., 98, 2024
8YE4
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BU of 8ye4 by Molmil
The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF
分子名称: Beta-2-microglobulin, MHC class I antigen precusor, Spike protein S1, ...
著者Deng, S.S, Jin, T.C, Xu, Z.H, Wang, M.H.
登録日2024-02-21
公開日2024-08-21
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.
J.Biol.Chem., 300, 2024

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件を2025-07-09に公開中

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