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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
8IOS
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BU of 8ios by Molmil
Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-1 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, Spike glycoprotein
著者Anraku, Y, Kita, S, Yajima, H, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
登録日2023-03-13
公開日2023-05-24
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (2.5 Å)
主引用文献Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants.
Nat Commun, 14, 2023
8IOU
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BU of 8iou by Molmil
Structure of SARS-CoV-2 XBB.1 spike glycoprotein in complex with ACE2 (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, Processed angiotensin-converting enzyme 2, ...
著者Anraku, Y, Kita, S, Yajima, H, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
登録日2023-03-13
公開日2023-05-24
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.18 Å)
主引用文献Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants.
Nat Commun, 14, 2023
8IOV
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Structure of SARS-CoV-2 XBB.1 spike RBD in complex with 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Anraku, Y, Kita, S, Yajima, H, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
登録日2023-03-13
公開日2023-05-24
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.29 Å)
主引用文献Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants.
Nat Commun, 14, 2023
8SPJ
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BU of 8spj by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) N28T Mutant
分子名称: 3C-like proteinase nsp5
著者Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
登録日2023-05-03
公開日2023-05-24
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (2.08 Å)
主引用文献Crystal Structure of SARS-CoV-2 Main Protease (Mpro) N28T Mutant
To Be Published
7VZT
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BU of 7vzt by Molmil
A human neutralizing antibody targeting SARS-CoV-2 RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GH12-Heavy, GH12-LIGHT, ...
著者Wang, F.Z, Wang, Y, Tan, X.W, Shi, R, Yan, J.H.
登録日2021-11-16
公開日2023-05-31
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (3.41 Å)
主引用文献GH12, glycosylation function
To Be Published
7XEG
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BU of 7xeg by Molmil
SARS-CoV-2-Beta-RBD and CB6-092-Fab complex
分子名称: CB6-092-Fab heavy chain, CB6-092-Fab light chain, Spike protein S1
著者Wang, Y, Feng, Y.
登録日2022-03-31
公開日2023-05-31
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.69 Å)
主引用文献SARS-CoV-2-Beta-RBD and CB6-092-Fab complex
To Be Published
7XEI
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BU of 7xei by Molmil
SARS-CoV-2-prototyped-RBD and CB6-092-Fab complex
分子名称: CB6-092-Fab heavy chain, CB6-092-Fab light chain, Spike protein S1
著者Wang, Y, Feng, Y.
登録日2022-03-31
公開日2023-05-31
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (2.76 Å)
主引用文献SARS-CoV-2-prototyped-RBD and CB6-092-Fab complex
To Be Published
7XMN
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BU of 7xmn by Molmil
Structure of SARS-CoV-2 ORF8
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, Maltodextrin-binding protein, ...
著者Chen, X, Xu, W.
登録日2022-04-26
公開日2023-05-31
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Glycosylated, Lipid-Binding, CDR-Like Domains of SARS-CoV-2 ORF8 Indicate Unique Sites of Immune Regulation.
Microbiol Spectr, 11, 2023
8H07
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SARS-CoV-2 BA.4 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C
分子名称: 10-5B H chain, 10-5B L chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Wang, X, Wang, Z.
登録日2022-09-28
公開日2023-05-31
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants.
Nat Commun, 14, 2023
8H08
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BU of 8h08 by Molmil
SARS-CoV-2 BA.1 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C
分子名称: 10-5B H chain, 10-5B L chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Wang, X, Wang, Z.
登録日2022-09-28
公開日2023-05-31
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants.
Nat Commun, 14, 2023
7WT7
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BU of 7wt7 by Molmil
SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (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, Heavy chain of Fab 9A8, ...
著者Wang, X, Wang, L.
登録日2022-02-04
公開日2023-06-07
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD.
Cell Discov, 8, 2022
7WT8
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BU of 7wt8 by Molmil
SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 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, Heavy chain of Fab 9A8, ...
著者Wang, X, Wang, L.
登録日2022-02-04
公開日2023-06-07
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD.
Cell Discov, 8, 2022
7WT9
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BU of 7wt9 by Molmil
SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8
分子名称: Heavy chain of Fab 9A8, Light chain of Fab 9A8, Spike glycoprotein
著者Wang, X, Wang, L.
登録日2022-02-04
公開日2023-06-07
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (4.3 Å)
主引用文献A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD.
Cell Discov, 8, 2022
7Y6D
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BU of 7y6d by Molmil
Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD
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Xu, J, Song, Y, Li, S.
登録日2022-06-20
公開日2023-06-07
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (4.39 Å)
主引用文献In situ architecture and membrane fusion of SARS-CoV-2 Delta variant.
Proc.Natl.Acad.Sci.USA, 120, 2023
8D55
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BU of 8d55 by Molmil
Closed state of SARS-CoV-2 BA.2 variant 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, J, Tang, W.C, Gao, H.L, Shi, W, Peng, H.Q, Volloch, S.R, Xiao, T.S, Chen, B.
登録日2022-06-04
公開日2023-06-07
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein.
Nat.Struct.Mol.Biol., 30, 2023
8D34
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Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A
分子名称: Uridylate-specific endoribonuclease nsp15
著者Farraj, R.A, Edwards, R.A, Glover, J.N.M.
登録日2022-05-31
公開日2023-06-14
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.91 Å)
主引用文献Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A
To Be Published
8DT8
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BU of 8dt8 by Molmil
LM18/Nb136 bispecific tetra-nanobody immunoglobulin in complex with SARS-CoV-2-6P-Mut7 S protein (focused refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, LM18 nanobody, Nb136 nanobody, ...
著者Ozorowski, G, Turner, H.L, Ward, A.B.
登録日2022-07-25
公開日2023-06-14
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.34 Å)
主引用文献Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins.
Proc.Natl.Acad.Sci.USA, 120, 2023
8ELH
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BU of 8elh by Molmil
Crystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANQF from SARS-CoV-2 virus
分子名称: ACETATE ION, Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, ...
著者Murdolo, L.D, Gras, S.
登録日2022-09-24
公開日2023-06-14
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.
Nature, 620, 2023
8EOO
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BU of 8eoo by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibodies WRAIR-2063 and WRAIR-2151
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Spike protein S1, ...
著者Jensen, J.L, Sankhala, R.S, Joyce, M.G.
登録日2022-10-03
公開日2023-06-14
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.77 Å)
主引用文献Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity.
J.Virol., 97, 2023
8SXO
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BU of 8sxo by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164I Mutant
分子名称: 3C-like proteinase nsp5
著者Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
登録日2023-05-23
公開日2023-06-14
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (2.76 Å)
主引用文献Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164I Mutant
To Be Published
7Y6L
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BU of 7y6l by Molmil
The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab816
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Ab816 heavy chain, Ab816 light chain, ...
著者Uchikubo, T, Shirouzu, M.
登録日2022-06-21
公開日2023-06-21
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents.
Iscience, 26, 2023
7Y6N
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BU of 7y6n by Molmil
The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab803
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Ab803 heavy chain, Ab803 light chain, ...
著者Uchikubo, T, Shirouzu, M.
登録日2022-06-21
公開日2023-06-21
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (4.4 Å)
主引用文献Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents.
Iscience, 26, 2023
8EPN
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BU of 8epn by Molmil
Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-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, Spike glycoprotein, ...
著者Williams, J.A, Harshbarger, W.
登録日2022-10-06
公開日2023-06-21
最終更新日2025-05-21
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity.
Sci Adv, 9, 2023
8HUR
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BU of 8hur by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with S217622
分子名称: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
著者Zhou, X.L, Zhang, J, Li, J.
登録日2022-12-24
公開日2023-06-21
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.64 Å)
主引用文献Structural basis for the inhibition of coronaviral main proteases by ensitrelvir.
Structure, 31, 2023
8IDN
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Cryo-EM structure of RBD/E77-Fab complex
分子名称: E77 Fab heavy chain, E77 Fab light chain, Spike protein S1, ...
著者Lu, D.F, Zhang, Z.C.
登録日2023-02-13
公開日2023-06-21
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.35 Å)
主引用文献The structure of the RBD-E77 Fab complex reveals neutralization and immune escape of SARS-CoV-2.
Acta Crystallogr D Struct Biol, 79, 2023

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件を2025-07-09に公開中

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