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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
7YQX
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BU of 7yqx by Molmil
SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state1)
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, S309 heavy chain, ...
著者Wang, L.
登録日2022-08-08
公開日2022-10-19
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.72 Å)
主引用文献Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75.
Cell Host Microbe, 30, 2022
7YQY
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SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state2)
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, S309 heavy chain, ...
著者Wang, L.
登録日2022-08-08
公開日2022-10-19
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.74 Å)
主引用文献Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75.
Cell Host Microbe, 30, 2022
7YR0
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BU of 7yr0 by Molmil
SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (interface)
分子名称: Heavy chain of S309, IGK@ protein, Spike protein S1, ...
著者Wang, L.
登録日2022-08-08
公開日2022-10-19
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.98 Å)
主引用文献Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75.
Cell Host Microbe, 30, 2022
7YR1
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BU of 7yr1 by Molmil
SARS-CoV-2 BA.2.75 S Trimer in complex with XG2v024
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, L.
登録日2022-08-08
公開日2022-10-19
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.62 Å)
主引用文献Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75.
Cell Host Microbe, 30, 2022
7YR2
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BU of 7yr2 by Molmil
SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state1)
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 2, ...
著者Wang, L.
登録日2022-08-08
公開日2022-10-19
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75.
Cell Host Microbe, 30, 2022
7YR3
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BU of 7yr3 by Molmil
SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state2)
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 2, ...
著者Wang, L.
登録日2022-08-08
公開日2022-10-19
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.52 Å)
主引用文献Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75.
Cell Host Microbe, 30, 2022
8D8Q
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BU of 8d8q by Molmil
SARS-CoV-2 Spike RBD in complex with DMAbs 2130 and 2196
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2130 heavy chain, 2130 light chain, ...
著者Du, J, Cui, J, Pallesen, J.
登録日2022-06-08
公開日2022-10-19
実験手法ELECTRON MICROSCOPY (4.2 Å)
主引用文献DNA-delivered antibody cocktail exhibits improved pharmacokinetics and confers prophylactic protection against SARS-CoV-2.
Nat Commun, 13, 2022
8D8R
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BU of 8d8r by Molmil
SARS-CoV-2 Spike RBD in complex with DMAb 2196
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2196 heavy chain, 2196 light chain, ...
著者Du, J, Cui, J, Pallesen, J.
登録日2022-06-08
公開日2022-10-19
実験手法ELECTRON MICROSCOPY (4.1 Å)
主引用文献DNA-delivered antibody cocktail exhibits improved pharmacokinetics and confers prophylactic protection against SARS-CoV-2.
Nat Commun, 13, 2022
7WB5
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BU of 7wb5 by Molmil
local structure of hu33 and spike
分子名称: Surface glycoprotein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, hu33 heavy chain, ...
著者Pulan, L.
登録日2021-12-15
公開日2022-10-26
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献A non-ACE2-blocking neutralizing antibody against Omicron-included SARS-CoV-2 variants.
Signal Transduct Target Ther, 7, 2022
7ZIT
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BU of 7zit by Molmil
14-3-3 in complex with SARS-COV2 N phospho-peptide
分子名称: 14-3-3 protein zeta/delta, ACETATE ION, BENZOIC ACID, ...
著者Eisenreichova, A, Boura, E.
登録日2022-04-08
公開日2022-10-26
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.79 Å)
主引用文献Structural basis for SARS-CoV-2 nucleocapsid (N) protein recognition by 14-3-3 proteins.
J.Struct.Biol., 214, 2022
8ERQ
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BU of 8erq by Molmil
SARS-CoV-2 BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment (local refinement of the RBD and S2X324)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, S2X324 Fab heavy chain, S2X324 Fab light chain, ...
著者Park, Y.J, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
登録日2022-10-12
公開日2022-10-26
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.
Science, 378, 2022
8ERR
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BU of 8err by Molmil
SARS-CoV-2 Omicron BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment
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, S2X324 heavy chain, ...
著者Park, Y.J, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
登録日2022-10-12
公開日2022-10-26
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.
Science, 378, 2022
8GS6
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BU of 8gs6 by Molmil
Structure of the SARS-CoV-2 BA.2.75 spike glycoprotein (closed state 1)
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Anraku, Y, Tabata-Sasaki, K, Kita, S, Fukuhara, H, Maenaka, K, Hashiguchi, T.
登録日2022-09-05
公開日2022-10-26
最終更新日2023-03-29
実験手法ELECTRON MICROSCOPY (2.86 Å)
主引用文献Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant.
Cell Host Microbe, 30, 2022
7WSH
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BU of 7wsh by Molmil
Cryo-EM structure of SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
著者Li, S, Han, P, Qi, J.
登録日2022-01-29
公開日2022-11-09
実験手法ELECTRON MICROSCOPY (2.89 Å)
主引用文献Cross-species recognition and molecular basis of SARS-CoV-2 and SARS-CoV binding to ACE2s of marine animals.
Natl Sci Rev, 9, 2022
7X26
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BU of 7x26 by Molmil
S41 neutralizing antibody Fab(MERS-CoV)
分子名称: Spike glycoprotein, antibody S41 heavy chain, antibody S41 light chain
著者Zeng, J.W, Zhang, S.Y, Wang, X.W.
登録日2022-02-25
公開日2022-11-09
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.685 Å)
主引用文献Cryoelectron microscopy structures of a human neutralizing antibody bound to MERS-CoV spike glycoprotein.
Front Microbiol, 13, 2022
7X2A
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BU of 7x2a by Molmil
MERS-CoV spike complex with S41 neutralizing antibody Fab Class1 (1u2d RBD with 1Fab)
分子名称: MERS-CoV Spike glycoprotein, antibody S41 heavy chain, antibody S41 light chain
著者Zeng, J.W, Zhang, S.Y, Zhou, H.X, Wang, X.W.
登録日2022-02-25
公開日2022-11-09
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (2.49 Å)
主引用文献Cryoelectron microscopy structures of a human neutralizing antibody bound to MERS-CoV spike glycoprotein.
Front Microbiol, 13, 2022
7ZR2
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BU of 7zr2 by Molmil
Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
分子名称: Spike protein S2', Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1
著者Camara-Artigas, A, Gavira, J.A, Cano-Munoz, M, Polo-Megias, D, Conejero-Lara, F.
登録日2022-05-03
公開日2022-11-09
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity.
Int.J.Biol.Macromol., 222, 2022
7Q3Q
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BU of 7q3q by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobody VHH-12
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, GLYCEROL, ...
著者Fernandez, I, Pederzoli, R, Rey, F.A.
登録日2021-10-28
公開日2022-11-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN
To Be Published
7Q3R
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BU of 7q3r by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobodies VHH-F04 and VHH-G09
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Spike glycoprotein, ...
著者Fernandez, I, Pederzoli, R, Rey, F.A.
登録日2021-10-28
公開日2022-11-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.92 Å)
主引用文献NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN
To Be Published
7SJ0
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BU of 7sj0 by Molmil
Antibody A7V3 bound to N-terminal domain of the spike
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, A7V3 Fab heavy chain, A7V3 Fab light chain, ...
著者Hsieh, C.-L, McLellan, J.S.
登録日2021-10-15
公開日2022-11-16
実験手法ELECTRON MICROSCOPY (3.36 Å)
主引用文献Antibody A7V3 bound to N-terminal domain of the spike
To Be Published
8EYJ
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BU of 8eyj by Molmil
Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S mutant in complex with 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
著者Noske, G.D, Godoy, A.S, Oliva, G.
登録日2022-10-27
公開日2022-11-16
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.738 Å)
主引用文献An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition.
Nat Commun, 14, 2023
7S83
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BU of 7s83 by Molmil
Crystal structure of SARS CoV-2 Spike Receptor Binding Domain in complex with shark neutralizing VNARs ShAb01 and ShAb02
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ShAb01 VNAR, ...
著者Chen, W.-H, Hajduczki, A, Dooley, H.M, Joyce, M.G.
登録日2021-09-17
公開日2022-11-23
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.52 Å)
主引用文献Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity.
Nat Commun, 14, 2023
7SIS
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BU of 7sis by Molmil
SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01
分子名称: ACETATE ION, Beta-2-microglobulin, CADMIUM ION, ...
著者Szeto, C, Gras, S.
登録日2021-10-14
公開日2022-11-23
最終更新日2024-05-15
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, 2024
7SWW
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BU of 7sww by Molmil
SARS-CoV-2 Spike NTD in complex with neutralizing Fab SARS2-57 (local refinement)
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, SARS2-57 Fv heavy chain, ...
著者Adams, L.J, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
登録日2021-11-21
公開日2022-11-23
最終更新日2023-02-01
実験手法ELECTRON MICROSCOPY (3.13 Å)
主引用文献A protective antibody targeting the N-terminal domain of SARS-CoV-2 spike recognizes most emerging variants
To Be Published
7SWX
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BU of 7swx by Molmil
SARS-CoV-2 Spike in complex with neutralizing Fab SARS2-57 (three down 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, SARS2-57 Fv heavy chain, ...
著者Adams, L.J, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
登録日2021-11-21
公開日2022-11-23
最終更新日2023-02-01
実験手法ELECTRON MICROSCOPY (3.13 Å)
主引用文献A protective antibody targeting the N-terminal domain of SARS-CoV-2 spike recognizes most emerging variants
To Be Published

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件を2024-09-25に公開中

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