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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
8CMD
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BU of 8cmd by Molmil
Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S761-775
分子名称: 1,2-ETHANEDIOL, HLA class II histocompatibility antigen, DR alpha chain, ...
著者MacLachlan, B.J, Mason, G.H, Sourfield, D.O, Godkin, A.J, Rizkallah, P.J.
登録日2023-02-19
公開日2023-07-26
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (2.54 Å)
主引用文献Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Cell Rep, 42, 2023
8CME
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BU of 8cme by Molmil
Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Membrane peptide M176-190
分子名称: 1,2-ETHANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, HLA class II histocompatibility antigen, ...
著者MacLachlan, B.J, Mason, G.H, Sourfield, D.O, Godkin, A.J, Rizkallah, P.J.
登録日2023-02-19
公開日2023-07-26
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (2.26 Å)
主引用文献Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Cell Rep, 42, 2023
8CMF
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BU of 8cmf by Molmil
Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp3 epitope (orf1ab)1350-1364
分子名称: 1,2-ETHANEDIOL, HLA class II histocompatibility antigen, DR alpha chain, ...
著者MacLachlan, B.J, Mason, G.H, Sourfield, D.O, Godkin, A.J, Rizkallah, P.J.
登録日2023-02-19
公開日2023-07-26
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Cell Rep, 42, 2023
8CMG
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BU of 8cmg by Molmil
Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide (orf1ab)6420-6434
分子名称: 1,2-ETHANEDIOL, HLA class II histocompatibility antigen, DR alpha chain, ...
著者MacLachlan, B.J, Mason, G.H, Sourfield, D.O, Godkin, A.J, Rizkallah, P.J.
登録日2023-02-19
公開日2023-07-26
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (1.64 Å)
主引用文献Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Cell Rep, 42, 2023
8CMH
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BU of 8cmh by Molmil
Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S486-505
分子名称: 1,2-ETHANEDIOL, 2-AMINO-ETHANETHIOL, HLA class II histocompatibility antigen, ...
著者MacLachlan, B.J, Mason, G.H, Sourfield, D.O, Godkin, A.J, Rizkallah, P.J.
登録日2023-02-19
公開日2023-07-26
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (1.64 Å)
主引用文献Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Cell Rep, 42, 2023
8CMI
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BU of 8cmi by Molmil
Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S761-775
分子名称: 1,2-ETHANEDIOL, HLA class II histocompatibility antigen, DR alpha chain, ...
著者MacLachlan, B.J, Mason, G.H, Sourfield, D.O, Godkin, A.J, Rizkallah, P.J.
登録日2023-02-19
公開日2023-07-26
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Cell Rep, 42, 2023
8FRJ
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Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SGC0946
分子名称: 5-bromo-7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine, Transcription factor ETV6,Guanine-N7 methyltransferase nsp14 chimera, ZINC ION
著者Kottur, J, Aggarwal, A.K.
登録日2023-01-07
公開日2023-07-26
最終更新日2023-09-27
実験手法X-RAY DIFFRACTION (1.57 Å)
主引用文献Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals.
Plos Pathog., 19, 2023
8FRK
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Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SGC8158
分子名称: 5'-S-(4-{[(4'-chloro[1,1'-biphenyl]-3-yl)methyl]amino}butyl)-5'-thioadenosine, ETHANOL, POTASSIUM ION, ...
著者Kottur, J, Aggarwal, A.K.
登録日2023-01-07
公開日2023-07-26
最終更新日2023-09-27
実験手法X-RAY DIFFRACTION (1.61 Å)
主引用文献Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals.
Plos Pathog., 19, 2023
7WQ8
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BU of 7wq8 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with Z-DEVD-FMK
分子名称: 3C-like proteinase, Z-DEVD-FMK
著者Wang, Y.C, Yang, C.S, Hou, M.H, Tsai, C.L, Chen, Y.
登録日2022-01-24
公開日2023-08-02
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Crystal structure of SARS-CoV-2 main protease in complex with Z-DEVD-FMK
To Be Published
7WQ9
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BU of 7wq9 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with Z-IETD-FMK
分子名称: 3C-like proteinase, Z-IETD-FMK
著者Wang, Y.C, Yang, C.S, Hou, M.H, Tsai, C.L, Chen, Y.
登録日2022-01-25
公開日2023-08-02
実験手法X-RAY DIFFRACTION (2.054 Å)
主引用文献Crystal structure of SARS-CoV-2 main protease in complex with Z-IETD-FMK
To Be Published
7WQB
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BU of 7wqb by Molmil
SARS-CoV-2 main protease mutant (P168A) in complex with MG-132
分子名称: 3C-like proteinase nsp5, MAGNESIUM ION, N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide
著者Wang, Y.C, Yang, C.S, Hou, M.H, Tsai, C.L, Chen, Y.
登録日2022-01-25
公開日2023-08-02
実験手法X-RAY DIFFRACTION (1.87 Å)
主引用文献SARS-CoV-2 main protease mutant (P168A) in complex with MG-132
To Be Published
7WQK
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BU of 7wqk by Molmil
wild-type SARS-CoV-2 main protease in complex with MG-132
分子名称: 3C-like proteinase, MAGNESIUM ION, N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide
著者Wang, Y.C, Yang, C.S, Hou, M.H, Tsai, C.L, Chen, Y.
登録日2022-01-25
公開日2023-08-02
実験手法X-RAY DIFFRACTION (2.15 Å)
主引用文献wild-type SARS-CoV-2 main protease in complex with MG-132
To Be Published
8DPZ
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BU of 8dpz by Molmil
Local refinement of SARS-CoV-2 vaccine induced antibody DH1338 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, DH1338 Fab Heavy Chain, DH1338 Fab Light Chain, ...
著者Stalls, V, May, A.J, Acharya, P.
登録日2022-07-18
公開日2023-08-02
実験手法ELECTRON MICROSCOPY (3.38 Å)
主引用文献Local refinement of SARS-CoV-2 vaccine induced antibody Ab026500 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain
To Be Published
8DTK
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BU of 8dtk by Molmil
Structure of RBD directed antibody DH1047 in complex with SARS-CoV-2 spike: Local refinement of RBD-Fab interace
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, DH1047 Fab Heavy Chain, DH1047 Fab Light Chain, ...
著者May, A.J, Manne, K, Acharya, P.
登録日2022-07-25
公開日2023-08-02
最終更新日2024-02-28
実験手法ELECTRON MICROSCOPY (3.77 Å)
主引用文献Broadly neutralizing antibody induction by non-stabilized SARS-CoV-2 Spike mRNA vaccination in nonhuman primates.
Biorxiv, 2023
8SPH
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BU of 8sph by Molmil
Crystal structure of chimeric omicron RBD (strain XBB.1) complexed with human ACE2
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, W, Shi, K, Aihara, H, Li, F.
登録日2023-05-03
公開日2023-08-02
最終更新日2023-09-13
実験手法X-RAY DIFFRACTION (2.71 Å)
主引用文献Structural evolution of SARS-CoV-2 omicron in human receptor recognition.
J.Virol., 97, 2023
8SPI
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BU of 8spi by Molmil
Crystal structure of chimeric omicron RBD (strain XBB.1.5) complexed with human ACE2
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, W, Shi, K, Aihara, H, Li, F.
登録日2023-05-03
公開日2023-08-02
最終更新日2023-09-13
実験手法X-RAY DIFFRACTION (3.06 Å)
主引用文献Structural evolution of SARS-CoV-2 omicron in human receptor recognition.
J.Virol., 97, 2023
7Y20
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BU of 7y20 by Molmil
S-ECD (Omicron BA.3) in complex with two PD of 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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2022-06-09
公開日2023-08-09
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Structural Basis for the Enhanced Infectivity and Immune Evasion of Omicron Subvariants.
Viruses, 15, 2023
7Y21
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BU of 7y21 by Molmil
S-ECD (Omicron BA.5) in complex with PD of 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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2022-06-09
公開日2023-08-09
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Structural Basis for the Enhanced Infectivity and Immune Evasion of Omicron Subvariants.
Viruses, 15, 2023
7YBH
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BU of 7ybh by Molmil
SARS-CoV-2 lambda variant spike
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Wang, X, Fu, W.
登録日2022-06-29
公開日2023-08-09
最終更新日2024-02-21
実験手法ELECTRON MICROSCOPY (3.5 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
7YBL
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BU of 7ybl by Molmil
SARS-CoV-2 B.1.620 variant spike (close 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2023-08-09
最終更新日2024-02-21
実験手法ELECTRON MICROSCOPY (3.6 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
7YBM
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BU of 7ybm by Molmil
SARS-CoV-2 C.1.2 variant spike (Close 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2023-08-09
最終更新日2024-02-21
実験手法ELECTRON MICROSCOPY (3.45 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
8FIV
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BU of 8fiv by Molmil
Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10541R
分子名称: (3Z)-N-([1,1'-biphenyl]-4-yl)-3-imino-N-[(1R)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]propanamide, 3C-like proteinase nsp5
著者Sacco, M, Wang, J, Chen, Y.
登録日2022-12-16
公開日2023-08-09
実験手法X-RAY DIFFRACTION (2.51 Å)
主引用文献Exploring diverse reactive warheads for the design of SARS-CoV-2 main protease inhibitors.
Eur.J.Med.Chem., 259, 2023
8FIW
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BU of 8fiw by Molmil
Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10221
分子名称: 3C-like proteinase nsp5, N-([1,1'-biphenyl]-4-yl)-N-[(1R)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]prop-2-enamide, N-([1,1'-biphenyl]-4-yl)-N-[(1S)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]prop-2-enamide
著者Sacco, M, Wang, J, Chen, Y.
登録日2022-12-16
公開日2023-08-09
実験手法X-RAY DIFFRACTION (2.54 Å)
主引用文献Exploring diverse reactive warheads for the design of SARS-CoV-2 main protease inhibitors.
Eur.J.Med.Chem., 259, 2023
8TBE
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BU of 8tbe by Molmil
Co-crystal structure of SARS-CoV-2 Mpro with Pomotrelvir
分子名称: 3C-like proteinase nsp5, Pomotrelvir bound form
著者Olland, A, Fontano, E, White, A.
登録日2023-06-28
公開日2023-08-09
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.15 Å)
主引用文献Evaluation of in vitro antiviral activity of SARS-CoV-2 M pro inhibitor pomotrelvir and cross-resistance to nirmatrelvir resistance substitutions.
Antimicrob.Agents Chemother., 67, 2023
8HR2
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BU of 8hr2 by Molmil
Ternary Crystal Complex Structure of RBD with NB1B5 and NB1C6
分子名称: NB1B5, NB1C6, Spike protein S1
著者Sun, Z.
登録日2022-12-14
公開日2023-08-16
実験手法X-RAY DIFFRACTION (1.94 Å)
主引用文献Structure basis of two nanobodies neutralizing SARS-CoV-2 Omicron variant by targeting ultra-conservative epitopes.
J.Struct.Biol., 215, 2023

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件を2024-07-10に公開中

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