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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
7OD3
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BU of 7od3 by Molmil
SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, LINOLEIC ACID, Spike glycoprotein
著者Toelzer, C, Gupta, K, Yadav, S.K.N, Borucu, U, Schaffitzel, C, Berger, I.
登録日2021-04-28
公開日2022-01-26
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2.
Nat Commun, 13, 2022
7ODL
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BU of 7odl by Molmil
SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C1 symmetry
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, LINOLEIC ACID, Spike glycoprotein
著者Toelzer, C, Gupta, K, Yadav, S.K.N, Borucu, U, Schaffitzel, C, Berger, I.
登録日2021-04-29
公開日2022-01-26
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2.
Nat Commun, 13, 2022
7QGI
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BU of 7qgi by Molmil
Crystal structure of SARS-CoV-2 NSP14 in the absence of NSP10
分子名称: PHOSPHATE ION, Proofreading exoribonuclease nsp14, ZINC ION
著者Newman, J.A, Imprachim, N, Yosaatmadja, Y, Gileadi, O.
登録日2021-12-08
公開日2022-01-26
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development.
Nucleic Acids Res., 51, 2023
7QO9
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BU of 7qo9 by Molmil
SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD and NTD (Local)
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 S Omicron Spike B.1.1.529, ...
著者Ni, D, Lau, K, Turelli, P, Beckert, B, Nazarov, S, Pojer, F, Myasnikov, A, Stahlberg, H, Trono, D.
登録日2021-12-23
公開日2022-01-26
実験手法ELECTRON MICROSCOPY (3.88 Å)
主引用文献Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion
Biorxiv, 2021
7TI9
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BU of 7ti9 by Molmil
Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2, form 2
分子名称: CHLORIDE ION, GLYCEROL, Papain-like protease nsp3
著者Stogios, P.J, Skarina, T, Di Leo, R, Savchenko, A, Joachimiak, A, Satchell, K.J.F, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2022-01-13
公開日2022-01-26
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.73 Å)
主引用文献Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2, form 2
To Be Published
7TLL
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BU of 7tll by Molmil
Structure of SARS-CoV-2 Mpro Omicron P132H 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Greasley, S.E, Ferre, R.A, Plotnikova, O, Liu, W, Stewart, A.E.
登録日2022-01-18
公開日2022-01-26
最終更新日2022-06-15
実験手法X-RAY DIFFRACTION (1.63 Å)
主引用文献Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants.
J.Biol.Chem., 298, 2022
7VJW
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BU of 7vjw by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.20 A resolution-10
分子名称: 3C-like proteinase
著者DeMirci, H, Ayan, E.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VJX
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BU of 7vjx by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.20 A resolution-12
分子名称: 3C-like proteinase
著者DeMirci, H, Usta, G.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VJY
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BU of 7vjy by Molmil
Crystal Structure of Sars-Cov-2 Mpro at 1.90 A resolution-1
分子名称: 3C-like proteinase
著者DeMirci, H, Johnson, A.J.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VJZ
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BU of 7vjz by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 1.90 A resolution-7
分子名称: 3C-like proteinase
著者DeMirci, H, Tokay, N.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK0
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BU of 7vk0 by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-6
分子名称: 3C-like proteinase
著者DeMirci, H, Cakilkaya, B.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK1
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BU of 7vk1 by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 1.93 A resolution-5
分子名称: 3C-like proteinase
著者DeMirci, H, Ertem, B.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.93 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK2
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BU of 7vk2 by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.0 A resolution -9
分子名称: 3C-like proteinase
著者DeMirci, H, Gul, M.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK3
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BU of 7vk3 by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-2
分子名称: 3C-like proteinase
著者DeMirci, H, Guven, O.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK4
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BU of 7vk4 by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-3
分子名称: 3C-like proteinase
著者DeMirci, H, Buyukdag, C.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK5
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BU of 7vk5 by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-8
分子名称: 3C-like proteinase
著者DeMirci, H, Gocenler, O.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.17 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK6
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BU of 7vk6 by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.25 A resolution-13
分子名称: 3C-like proteinase
著者DeMirci, H, Yuksel, B.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK7
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BU of 7vk7 by Molmil
Crystal Structure of SARS-CoV-2 Mpro at 2.4 A resolution-11
分子名称: 3C-like proteinase
著者DeMirci, H, Dag, C.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7VK8
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BU of 7vk8 by Molmil
Crystal structure of SARS-CoV-2 Mpro at 2.4 A Resolution
分子名称: 3C-like proteinase
著者DeMirci, H, Usta, G.
登録日2021-09-29
公開日2022-01-26
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Crystals, 11, 2021
7WEV
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BU of 7wev by Molmil
SARS-COV-2 BETA VARIANT SPIKE PROTEIN IN TRANSITION STATE
分子名称: Spike glycoprotein
著者Xu, C, Cong, Y.
登録日2021-12-24
公開日2022-01-26
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7WK2
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BU of 7wk2 by Molmil
SARS-CoV-2 Omicron S-close
分子名称: Spike glycoprotein
著者Li, J.W, Cong, Y.
登録日2022-01-08
公開日2022-01-26
最終更新日2022-05-04
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Molecular basis of receptor binding and antibody neutralization of Omicron.
Nature, 604, 2022
7WK3
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BU of 7wk3 by Molmil
SARS-CoV-2 Omicron S-open
分子名称: Spike glycoprotein
著者Li, J.W, Cong, Y.
登録日2022-01-08
公開日2022-01-26
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Structural basis for ACE2 engagement and antibody evasion and neutralization of SARS-Co-2 Omicron varient
To Be Published
7WK8
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BU of 7wk8 by Molmil
SARS-CoV-2 Omicron spike protein SD1 in complex with S3H3 Fab
分子名称: Heavy chain of S3H3 Fab, Light chain of S3H3 Fab, Spike glycoprotein
著者Hong, Q, Cong, Y.
登録日2022-01-08
公開日2022-01-26
最終更新日2022-05-04
実験手法ELECTRON MICROSCOPY (3.61 Å)
主引用文献Molecular basis of receptor binding and antibody neutralization of Omicron.
Nature, 604, 2022
7WKA
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BU of 7wka by Molmil
SARS-CoV-2 Omicron closed state spike protein in complex with S3H3 Fab
分子名称: Heavy chain of S3H3 Fab, Light chain of S3H3 Fab, Spike glycoprotein
著者Hong, Q, Cong, Y.
登録日2022-01-08
公開日2022-01-26
最終更新日2022-05-04
実験手法ELECTRON MICROSCOPY (3.64 Å)
主引用文献Molecular basis of receptor binding and antibody neutralization of Omicron.
Nature, 604, 2022
7F7E
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BU of 7f7e by Molmil
SARS-CoV-2 S protein RBD in complex with A5-10 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of A5-10 Fab, Light chain of A5-10 Fab, ...
著者Dou, Y, Wang, X, Wang, K, Liu, P, Lu, B.
登録日2021-06-29
公開日2022-02-02
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.49 Å)
主引用文献Etesevimab in combination with JS026 neutralizing SARS-CoV-2 and its variants.
Emerg Microbes Infect, 11, 2022

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件を2024-08-07に公開中

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