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新型コロナウイルスの構造情報

このページの他言語版もあります: English简体中文繁體中文한국어
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
8DLO
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BU of 8dlo by Molmil
Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein
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Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.25 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLP
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BU of 8dlp by Molmil
Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human 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Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.64 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLQ
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BU of 8dlq by Molmil
Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.77 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLR
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BU of 8dlr by Molmil
Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8 (focused refinement of NTD and 4-8)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab 4-8 heavy chain, Fab 4-8 light chain, ...
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.51 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLS
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BU of 8dls by Molmil
Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8)
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, Fab 4A8 heavy chain, ...
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.66 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLT
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BU of 8dlt by Molmil
Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein
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Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.4 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLU
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BU of 8dlu by Molmil
Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with human 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Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (3.14 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLV
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BU of 8dlv by Molmil
Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (3.11 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLW
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BU of 8dlw by Molmil
Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with Fab S2M11
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, Fab S2M11 heavy chain, ...
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.16 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLX
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BU of 8dlx by Molmil
Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with VH ab6
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Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.45 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLY
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BU of 8dly by Molmil
Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with VH ab6 (focused refinement of NTD and VH ab6)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, VH ab6
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLZ
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BU of 8dlz by Molmil
Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6
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Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (2.57 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DM0
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BU of 8dm0 by Molmil
Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6 (focused refinement of NTD and VH ab6)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, VH ab6
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-07-08
公開日2022-08-31
実験手法ELECTRON MICROSCOPY (3.21 Å)
主引用文献SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DV1
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BU of 8dv1 by Molmil
SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion,Immunoglobulin gamma-1 heavy chain, Spike glycoprotein
著者QCRG Structural Biology Consortium, Remesh, S.G, Merz, G.E, Brilot, A.F, Chio, U, Verba, K.A.
登録日2022-07-27
公開日2022-08-31
最終更新日2023-03-15
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.
Structure, 31, 2023
8DV2
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BU of 8dv2 by Molmil
SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to computationally engineered ACE2 mimetic CVD293
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion, Spike glycoprotein
著者QCRG Structural Biology Consortium, Remesh, S.G, Merz, G.E, Brilot, A.F, Chio, U, Verba, K.A.
登録日2022-07-27
公開日2022-08-31
最終更新日2023-03-15
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.
Structure, 31, 2023
8DZH
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BU of 8dzh by Molmil
Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with two RBDs down in complex with the Fab fragment of human neutralizing antibody MB.02
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Hu, Y, Xiong, Y.
登録日2022-08-07
公開日2022-08-31
最終更新日2023-11-15
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages.
Signal Transduct Target Ther, 8, 2023
8DZI
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BU of 8dzi by Molmil
Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody MB.02
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Hu, Y, Xiong, Y.
登録日2022-08-07
公開日2022-08-31
最終更新日2023-11-15
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages.
Signal Transduct Target Ther, 8, 2023
7PHZ
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BU of 7phz by Molmil
Crystal structure of X77 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in spacegroup P2(1)2(1)2(1).
分子名称: 1,2-ETHANEDIOL, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
著者Costanzi, E, Demitri, N, Storici, P.
登録日2021-08-19
公開日2022-09-07
最終更新日2024-05-01
実験手法X-RAY DIFFRACTION (1.66 Å)
主引用文献Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease.
J.Chem.Inf.Model., 64, 2024
7TW7
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BU of 7tw7 by Molmil
Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SAM
分子名称: S-ADENOSYLMETHIONINE, Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera, ZINC ION
著者Kottur, J, Aggarwal, A.K.
登録日2022-02-06
公開日2022-09-07
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.62 Å)
主引用文献High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.
Nat.Struct.Mol.Biol., 29, 2022
7TW8
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BU of 7tw8 by Molmil
Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SAH
分子名称: S-ADENOSYL-L-HOMOCYSTEINE, Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera, ZINC ION
著者Kottur, J, Aggarwal, A.K.
登録日2022-02-06
公開日2022-09-07
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.
Nat.Struct.Mol.Biol., 29, 2022
7TW9
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BU of 7tw9 by Molmil
Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to Sinefungin
分子名称: DI(HYDROXYETHYL)ETHER, ETHANOL, METHANOL, ...
著者Kottur, J, Aggarwal, A.K.
登録日2022-02-06
公開日2022-09-07
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.41 Å)
主引用文献High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.
Nat.Struct.Mol.Biol., 29, 2022
8CZI
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BU of 8czi by Molmil
Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with extended HR2
分子名称: Scaffolded Spike protein S2' HR1, Spike protein S2' HR2
著者Yang, K, Brunger, A.T.
登録日2022-05-24
公開日2022-09-07
最終更新日2024-06-12
実験手法ELECTRON MICROSCOPY (2.22 Å)
主引用文献Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein.
Proc.Natl.Acad.Sci.USA, 119, 2022
8E5X
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BU of 8e5x by Molmil
Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl sulfinyl benzene inhibitor
分子名称: (2~{S})-2-[[(2~{S})-4-methyl-2-[[2-methyl-2-[oxidanyl(phenyl)-$l^{3}-sulfanyl]propoxy]carbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase, N~2~-(ethoxycarbonyl)-N-{(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide, ...
著者Lovell, S, Machen, A.J, Battaile, K.P, Dampalla, C.S, Groutas, W.C.
登録日2022-08-22
公開日2022-09-07
最終更新日2024-05-01
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV).
Eur.J.Med.Chem., 254, 2023
8E61
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BU of 8e61 by Molmil
Crystal structure of SARS-CoV-2 3CL protease in complex with a m-chlorophenyl dimethyl sulfane inhibitor
分子名称: (1R,2S)-2-{[N-({2-[(3-chlorophenyl)sulfanyl]-2-methylpropoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-2-{[N-({2-[(3-chlorophenyl)sulfanyl]-2-methylpropoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase, ...
著者Lovell, S, Liu, L, Battaile, K.P, Madden, T.K, Groutas, W.C.
登録日2022-08-22
公開日2022-09-07
最終更新日2024-05-01
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV).
Eur.J.Med.Chem., 254, 2023
7F60
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BU of 7f60 by Molmil
Crystal structure of auxiliary protein in complex with human nuclear protein
分子名称: Nuclear pore complex protein Nup98-Nup96, ORF6 protein, mRNA export factor
著者Gao, X, Cui, S.
登録日2021-06-23
公開日2022-09-14
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.85 Å)
主引用文献Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport
Nat Commun, 13, 2022

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件を2024-08-07に公開中

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