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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
9B0Y
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BU of 9b0y by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Singh, S, Hasan, S.S.
登録日2024-03-12
公開日2025-03-05
最終更新日2025-03-19
実験手法ELECTRON MICROSCOPY (2.32 Å)
主引用文献Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9BJ2
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Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1533 (local refinement of NTD and C1533)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, C1533 Heavy Chain, C1533 Light Chain, ...
著者Rubio, A.A, Abernathy, M.E, Barnes, C.O.
登録日2024-04-24
公開日2025-03-05
最終更新日2025-03-19
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9BJ3
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Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1596
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, C1596 Fab Heavy Chain, ...
著者Rubio, A.A, Abernathy, M.E, Barnes, C.O.
登録日2024-04-24
公開日2025-03-05
最終更新日2025-03-19
実験手法ELECTRON MICROSCOPY (3.04 Å)
主引用文献Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9BJ4
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Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C952
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C952 Heavy Chain, C952 Light Chain, ...
著者Rubio, A.A, Abernathy, M.E, Barnes, C.O.
登録日2024-04-24
公開日2025-03-05
最終更新日2025-03-19
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9CXE
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BU of 9cxe by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation -C1
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Singh, S, Hasan, S.S.
登録日2024-07-31
公開日2025-03-05
最終更新日2025-03-19
実験手法ELECTRON MICROSCOPY (2.48 Å)
主引用文献Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9I81
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SARS-CoV-2 RdRp bound to a stack of three HeE1-2Tyr molecules
分子名称: N-[8-(cyclohexyloxy)-1-oxo-2-phenyl-1H-pyrido[2,1-b][1,3]benzothiazole-4-carbonyl]-L-tyrosine, Non-structural protein 7, Non-structural protein 8, ...
著者Kabinger, F, Doze, V, Schmitzova, J, Lidschreiber, M, Dienemann, C, Cramer, P.
登録日2025-02-04
公開日2025-03-05
最終更新日2025-03-26
実験手法ELECTRON MICROSCOPY (2.98 Å)
主引用文献Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr.
Proc.Natl.Acad.Sci.USA, 122, 2025
8YK4
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BU of 8yk4 by Molmil
Structure of SARS-CoV-2 RBD and antibody NT-108
分子名称: Spike protein S1, antibody NT-108, single chain Fv fragment
著者Anraku, Y, Kita, S, Onodera, T, Sato, A, Tadokoro, T, Adachi, Y, Ito, S, Suzuki, T, Sasaki, J, Shiwa, N, Iwata, N, Nagata, N, Kazuki, Y, Oshimura, M, Sasaki, M, Orba, Y, Suzuki, T, Sawa, H, Hashiguchi, T, Fukuhara, H, Takahashi, Y, Maenaka, K.
登録日2024-03-04
公開日2025-03-12
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Structural Basis for Potent Neutralization Activity of SARS-CoV-2 Antibody, NT-108
To Be Published
8YKG
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Structure of SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (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, NT-108 scFv, ...
著者Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K.
登録日2024-03-05
公開日2025-03-12
実験手法ELECTRON MICROSCOPY (3.28 Å)
主引用文献Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
8YKH
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BU of 8ykh by Molmil
Structure of SARS-CoV-2 spike RBD in complex with NT-108 scFv
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NT-108 scFv, Spike glycoprotein
著者Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K.
登録日2024-03-05
公開日2025-03-12
実験手法ELECTRON MICROSCOPY (3.27 Å)
主引用文献Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
9BLL
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BU of 9bll by Molmil
Cryo-EM of RBD(EG5.1)/1301B7 Fab Complex
分子名称: 1301B7 Heavy Chain, 1301B7 Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Walter, M.R, Green, T.J.
登録日2024-04-30
公開日2025-03-12
実験手法ELECTRON MICROSCOPY (4.1 Å)
主引用文献Potent neutralization by a RBD antibody with broad specificity for SARS-CoV-2 JN.1 and other variants.
Npj Viruses, 2, 2024
9CCI
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BU of 9cci by Molmil
Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, M39 Fab heavy chain, M39 Fab light chain, ...
著者Bajic, G, Jaiswal, D.
登録日2024-06-21
公開日2025-03-12
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (2.65 Å)
主引用文献Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.
Biorxiv, 2024
9CCJ
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Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2
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, M2 Fab Heavy Chain, ...
著者Bajic, G, Civljak, A.
登録日2024-06-21
公開日2025-03-12
実験手法ELECTRON MICROSCOPY (2.37 Å)
主引用文献Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.
Biorxiv, 2024
9CGV
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BU of 9cgv by Molmil
SARS-CoV-2 nsp12 NiRAN domain bound to a covalent inhibitor SW090466-1
分子名称: MANGANESE (II) ION, Non-structural protein 7, Non-structural protein 8, ...
著者Osinski, A, Hernandez, G, Tagliabracci, V.S.
登録日2024-07-01
公開日2025-03-12
最終更新日2025-04-23
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine.
J.Biol.Chem., 301, 2025
9J66
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BU of 9j66 by Molmil
Cryo-EM structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment CAV-C65 (local refinement)
分子名称: CAV-C65 Heavy chain, CAV-C65 Light chain, Spike protein S1
著者Jing, X, Chen, Y, Gong, P.
登録日2024-08-15
公開日2025-03-12
実験手法ELECTRON MICROSCOPY (3.55 Å)
主引用文献IgA class switching enhances neutralizing potency against SARS-CoV-2 by increased antibody hinge flexibility.
Antiviral Res., 235, 2025
9N55
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BU of 9n55 by Molmil
X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
分子名称: N-OCTANE, ORF9b protein
著者San Felipe, C.J, Fraser, J.S.
登録日2025-02-03
公開日2025-03-12
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
To Be Published
8UTC
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HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
分子名称: Beta-2-microglobulin, CHLORIDE ION, HLA class I histocompatibility antigen, ...
著者Oltean, N, Nyovanie, S, Hashem, A, Patskovska, L, Patskovsky, Y, Krogsgaard, M.
登録日2023-10-30
公開日2025-03-19
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
To Be Published
8Z1H
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BU of 8z1h by Molmil
Crystal structure of SARS main protease in complex with PF-00835231
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Lin, C, Zhang, J, Li, J.
登録日2024-04-11
公開日2025-03-19
実験手法X-RAY DIFFRACTION (2.61 Å)
主引用文献Crystal structure of SARS main protease in complex with PF-00835231
To Be Published
9DJ8
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RNA-nsp9 bound to the NiRAN domain of the E-RTC with an empty G-pocket
分子名称: ADENOSINE MONOPHOSPHATE, Non-structural protein 9, RNA-directed RNA polymerase, ...
著者Small, G.I, Darst, S.A, Campbell, E.A.
登録日2024-09-06
公開日2025-03-19
実験手法ELECTRON MICROSCOPY (2.58 Å)
主引用文献Matters arising: There is no structure of the catalytic intermediate of GTP-mediated mRNA capping by the SARS-CoV-2 NiRAN domain, and thus the mechanism remains unknown
To Be Published
9L09
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BU of 9l09 by Molmil
SARS-CoV-2 C-RTC with 13-TP
分子名称: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
著者Huang, Y.C, Liang, L, Liu, Y.X, Yan, L.M, Lou, Z.Y, Rao, Z.H.
登録日2024-12-12
公開日2025-03-19
最終更新日2025-03-26
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Discovery of a 2'-a-Fluoro-2'-b-C-(fluoromethyl) Purine Nucleotide Prodrug as a Potential Oral Anti-SARS-CoV-2 Agent
J Med Chem, 68, 2025
9L6C
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BU of 9l6c by Molmil
Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Fab ConD-852, Heavy chain of Fab P2C-1F11, ...
著者Zheng, Z, Bing, J, Congcong, L, Bing, Z.
登録日2024-12-24
公開日2025-03-19
実験手法ELECTRON MICROSCOPY (3.33 Å)
主引用文献Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs
To Be Published
8ZYF
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BU of 8zyf by Molmil
Crystal structure of ZW2G10 Fab in complex with omicron RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, ZW2G10 fab heavy chain, ...
著者Yuan, H.Y, Li, J.M.
登録日2024-06-17
公開日2025-03-26
最終更新日2025-04-16
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Nasal delivery of secretory IgA confers enhanced neutralizing activity against Omicron variants compared to its IgG counterpart.
Mol.Ther., 33, 2025
9GXE
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BU of 9gxe by Molmil
Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
分子名称: 2,4,6-tris(chloromethyl)-1,3,5-triazine, 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Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A.
登録日2024-09-30
公開日2025-03-26
実験手法ELECTRON MICROSCOPY (2.3 Å)
主引用文献Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
To Be Published
9GXG
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Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
分子名称: 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone, 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A.
登録日2024-09-30
公開日2025-03-26
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (1.92 Å)
主引用文献Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
To Be Published
8YWE
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BU of 8ywe by Molmil
Local refinement of SARS-CoV-2 Omicron BA.2.86 S complexed with Abs G7-Fc
分子名称: 7F3 scFv, GW01 scFv, Spike protein S1
著者Ma, Y, Liu, Q, Rehati, P, Zhang, Z.
登録日2024-03-31
公開日2025-04-02
実験手法ELECTRON MICROSCOPY (2.69 Å)
主引用文献Impact of scFv Sequence and Position on the Functionality of Bispecific Antibodies against Omicron Variants EG.5 and BA.2.86
To Be Published
8ZFV
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BU of 8zfv by Molmil
Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone
分子名称: Ceftriaxone, DI(HYDROXYETHYL)ETHER, Nucleoprotein, ...
著者Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
登録日2024-05-08
公開日2025-04-02
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
J.Struct.Biol., 217, 2025

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件を2025-07-09に公開中

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