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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
9AVQ
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BU of 9avq by Molmil
Crystal structure of SARS-CoV-2 main protease A191T mutant in complex with an inhibitor Nirmatrelvir
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, DI(HYDROXYETHYL)ETHER
著者Bulut, H, Hattori, S, Hayashi, H, Hasegawa, K, Li, M, Wlodawer, A, Tamamura, H, Mitsuya, H.
登録日2024-03-04
公開日2024-04-24
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.58 Å)
主引用文献Structural and virologic mechanism of the emergence of resistance to M pro inhibitors in SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 121, 2024
8J36
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Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with PF00835231
分子名称: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
著者Zhou, X.L, Lin, C, Zou, X.F, Zhang, J, Li, J.
登録日2023-04-16
公開日2024-05-01
最終更新日2025-05-07
実験手法X-RAY DIFFRACTION (2.21 Å)
主引用文献Structural basis for the inhibition of coronaviral main proteases by PF-00835231.
Acta Biochim.Biophys.Sin., 56, 2024
8SH8
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BU of 8sh8 by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain Asn40Asp mutant in complex with ADP-ribose (P43 crystal form)
分子名称: Papain-like protease nsp3, [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
著者Correy, G.J, Fraser, J.S.
登録日2023-04-13
公開日2024-05-01
実験手法X-RAY DIFFRACTION (0.9 Å)
主引用文献Crystal structure of SARS-CoV-2 NSP3 macrodomain Asn40Asp mutant in complex with ADP-ribose (P43 crystal form)
To Be Published
8VQR
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BU of 8vqr by Molmil
Crystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric raccoon dog ACE2
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Hsueh, F.-C, Shi, K, Aihara, H, Li, F.
登録日2024-01-19
公開日2024-05-01
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.565 Å)
主引用文献Structural basis for raccoon dog receptor recognition by SARS-CoV-2.
Plos Pathog., 20, 2024
8XLM
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BU of 8xlm by Molmil
Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-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, Processed angiotensin-converting enzyme 2, ...
著者Nomai, T, Anraku, Y, Kita, S, Hashiguchi, T, Maenaka, K.
登録日2023-12-26
公開日2024-05-01
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.22 Å)
主引用文献Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant.
Microbiol Immunol, 68, 2024
8XLN
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BU of 8xln by Molmil
Structure of the SARS-CoV-2 EG.5.1 spike RBD in complex with 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Nomai, T, Anraku, Y, Kita, S, Hashiguchi, T, Maenaka, K.
登録日2023-12-26
公開日2024-05-01
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.78 Å)
主引用文献Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant.
Microbiol Immunol, 68, 2024
8OWT
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BU of 8owt by Molmil
SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody A8, ...
著者Mikolajek, H, Naismith, J.H, Owens, R.J.
登録日2023-04-28
公開日2024-05-08
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.37 Å)
主引用文献Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2.
Open Biology, 14, 2024
8OWV
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BU of 8owv by Molmil
H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, F2, GLYCEROL, ...
著者Mikolajek, H, Naismith, J.H, Owens, R.J.
登録日2023-04-28
公開日2024-05-08
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (1.73 Å)
主引用文献Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2.
Open Biology, 14, 2024
8OWW
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BU of 8oww by Molmil
B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan)
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, B5-5 nanobody, ...
著者Cornish, K.A.S, Naismith, J.H, Owens, R.J.
登録日2023-04-28
公開日2024-05-08
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.969 Å)
主引用文献Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2.
Open Biology, 14, 2024
8QRF
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BU of 8qrf by Molmil
SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs
分子名称: Beta-49 heavy chain, Beta-49 light chain, Spike protein S1, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2023-10-06
公開日2024-05-08
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (3.7 Å)
主引用文献A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
Cell Rep Med, 5, 2024
8QRG
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BU of 8qrg by Molmil
SARS-CoV-2 delta RBD complexed with XBB-2 Fab and NbC1
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, NbC1, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2023-10-07
公開日2024-05-08
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
Cell Rep Med, 5, 2024
8QSQ
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BU of 8qsq by Molmil
Locally refined SARS-CoV-2 BA-2.86 Spike receptor binding domain (RBD) complexed with angiotensin converting enzyme 2 (ACE2)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S2'
著者Ren, J, Stuart, D.I, Duyvesteyn, H.M.E.
登録日2023-10-11
公開日2024-05-08
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
Cell Rep Med, 5, 2024
8QTD
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BU of 8qtd by Molmil
Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab
分子名称: Spike glycoprotein,Fibritin, XBB-7 fab heavy chain, XBB-7 fab light chain
著者Ren, J, Duyvesteyn, H.M.E, Stuart, D.I.
登録日2023-10-12
公開日2024-05-08
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
Cell Rep Med, 5, 2024
8R80
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BU of 8r80 by Molmil
SARS-CoV-2 Delta RBD in complex with XBB-9 Fab and an anti-Fab nanobody
分子名称: Spike protein S1, XBB-9 Fab heavy chain, XBB-9 Fab light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2023-11-27
公開日2024-05-08
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (4.03 Å)
主引用文献A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
Cell Rep Med, 5, 2024
8R8K
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BU of 8r8k by Molmil
XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
分子名称: Spike glycoprotein,Fibritin, XBB-4 Fab Heavy chain, XBB-4 Fab Light chain
著者Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
登録日2023-11-29
公開日2024-05-08
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.41 Å)
主引用文献A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
Cell Rep Med, 5, 2024
8YSA
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BU of 8ysa by Molmil
The co-crystal structure of SARS-CoV-2 Mpro in complex with compound H102
分子名称: 3C-like proteinase nsp5, BOC-TBG-PHE-ELL
著者Zheng, W.Y, Fu, L.F, Feng, Y, Han, P, Qi, J.X.
登録日2024-03-22
公開日2024-05-08
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Discovery, Biological Activity, and Structural Mechanism of a Potent Inhibitor of SARS-CoV-2 Main Protease
To Be Published
8OYU
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BU of 8oyu by Molmil
Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '2 up 1 down' RBD conformation
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, H6 nanobody, ...
著者Weckener, M, Naismith, J.H, Owens, R.J.
登録日2023-05-05
公開日2024-05-15
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2.
Open Biology, 14, 2024
8RBU
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BU of 8rbu by Molmil
Crystal structure of HLA-A*11:01 in complex with SVLNDILARL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
分子名称: 1,2-ETHANEDIOL, Beta-2-microglobulin, CHLORIDE ION, ...
著者Ahn, Y.M, Maddumage, J.C, Szeto, C, Gras, S.
登録日2023-12-05
公開日2024-05-15
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Curr Res Struct Biol, 7, 2024
8RBV
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BU of 8rbv by Molmil
SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by HLA-A*02:01
分子名称: 1,2-ETHANEDIOL, ACETATE ION, Beta-2-microglobulin, ...
著者Ahn, Y.M, Maddumage, J.C, Szeto, C, Gras, S.
登録日2023-12-05
公開日2024-05-15
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Curr Res Struct Biol, 7, 2024
8RCV
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BU of 8rcv by Molmil
Crystal structure of HLA B*13:01 in complex with SVLNDIFSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
分子名称: 1,2-ETHANEDIOL, Beta-2-microglobulin, HLA class I histocompatibility antigen B alpha chain, ...
著者Ahn, Y.M, Maddumage, J.C, Szeto, C, Gras, S.
登録日2023-12-07
公開日2024-05-15
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Curr Res Struct Biol, 7, 2024
8REF
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BU of 8ref by Molmil
Crystal structure of HLA B*13:01 in complex with SVLNDILARL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
分子名称: 1,2-ETHANEDIOL, Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, ...
著者Ahn, Y.M, Maddumage, J.C, Szeto, C, Gras, S.
登録日2023-12-11
公開日2024-05-15
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Curr Res Struct Biol, 7, 2024
8RH6
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BU of 8rh6 by Molmil
Crystal structure of HLA-A*11:01 in complex with SVLNDILSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
分子名称: 1,2-ETHANEDIOL, Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, ...
著者Ahn, Y.M, Maddumage, J.C, Szeto, C, Gras, S.
登録日2023-12-15
公開日2024-05-15
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (3.32 Å)
主引用文献The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Curr Res Struct Biol, 7, 2024
8RHQ
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BU of 8rhq by Molmil
Crystal structure of HLA-A*11:01 in complex with SVLNDIFSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
分子名称: 1,2-ETHANEDIOL, Beta-2-microglobulin, CHLORIDE ION, ...
著者Ahn, Y.M, Maddumage, J.C, Szeto, C, Gras, S.
登録日2023-12-16
公開日2024-05-15
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Curr Res Struct Biol, 7, 2024
8SUO
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BU of 8suo by Molmil
BA.2/AZD1061/AZD3152 structure analysis
分子名称: AZD1061 heavy chain, AZD1061 light chain, AZD3152 heavy chain, ...
著者Oganesyan, V, van Dyk, N, Dippel, A, Barnes, A, O'Connor, E.
登録日2023-05-12
公開日2024-05-15
最終更新日2024-11-27
実験手法X-RAY DIFFRACTION (3.3 Å)
主引用文献AZD3152 neutralizes SARS-CoV-2 historical and contemporary variants and is protective in hamsters and well tolerated in adults.
Sci Transl Med, 16, 2024
8ZBY
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BU of 8zby by Molmil
SARS-CoV-2 Omicron BA.1 spike trimer (x2-4P) in complex with 3 D1F6 Fabs (0 RBD up)
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 D1F6 Fab, ...
著者Liu, B, Gao, X, Li, Z, Chen, Q, He, J, Xiong, X.
登録日2024-04-28
公開日2024-05-15
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.67 Å)
主引用文献An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike.
Cell Rep, 43, 2024

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件を2025-07-09に公開中

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