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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
7P2O
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NMR solution structure of SUD-C domain of SARS-CoV-2
分子名称: Non-structural protein 3
著者Gallo, A, Tsika, A.C, Fourkiotis, N.K, Spyroulias, G.A.
登録日2021-07-06
公開日2022-07-20
最終更新日2024-06-19
実験手法SOLUTION NMR
主引用文献NMR solution structure of SUD-C domain of SARS-CoV-2
To Be Published
7SKZ
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BU of 7skz by Molmil
Crystal Structure of VN01H1 Fab in complex with SARS-CoV-2 S fusion peptide
分子名称: Heavy chain of VN01H1 Fab, Light chain of VN01H1 Fab, PRO-SER-LYS-ARG-SER-PHE-ILE-GLU-ASP-LEU-LEU-PHE-ASN
著者Tortorici, M.A, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2021-10-22
公開日2022-07-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.86 Å)
主引用文献ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.
Science, 377, 2022
7SL5
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Crystal Structure of VP12E7 Fab in complex with SARS-CoV-2 S fusion peptide
分子名称: Heavy chain VP12E7 Fab, Light chain VP12E7 Fab, PRO-SER-LYS-ARG-SER-PHE-ILE-GLU-ASP-LEU-LEU-PHE-ASN
著者Tortorici, M.A, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2021-10-22
公開日2022-07-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.
Science, 377, 2022
7VQ0
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Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86
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Maeda, R, Fujita, J, Konishi, Y, Kazuma, Y, Yamazaki, H, Anzai, I, Yamaguchi, K, Kasai, K, Nagata, K, Yamaoka, Y, Miyakawa, K, Ryo, A, Shirakawa, K, Makino, F, Matsuura, Y, Inoue, T, Imura, A, Namba, K, Takaori-Kondo, A.
登録日2021-10-18
公開日2022-07-20
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.
Commun Biol, 5, 2022
7WO5
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SARS-CoV-2 Spike in complex with IgG 553-15 (S-553-15 trimer)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, mAb15 VH, ...
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2022-01-20
公開日2022-07-20
最終更新日2022-09-14
実験手法ELECTRON MICROSCOPY (3.45 Å)
主引用文献Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer.
J.Virol., 96, 2022
7WO7
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Locally refined region of SARS-CoV-2 Spike in complex with IgG 553-15
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, mAb15 VH, ...
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2022-01-20
公開日2022-07-20
最終更新日2022-09-14
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer.
J.Virol., 96, 2022
7WOB
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SARS-CoV-2 Spike in complex with IgG 553-60 (2-up trimer)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, mAb60 VH, ...
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2022-01-21
公開日2022-07-20
最終更新日2022-09-14
実験手法ELECTRON MICROSCOPY (3.25 Å)
主引用文献Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer.
J.Virol., 96, 2022
7WOC
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Locally refined region of SARS-CoV-2 Spike in complex with IgG 553-60
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, mAb60 VH, ...
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2022-01-21
公開日2022-07-20
最終更新日2022-09-14
実験手法ELECTRON MICROSCOPY (3.35 Å)
主引用文献Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer.
J.Virol., 96, 2022
7WOG
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SARS-CoV-2 Omicron S monomer complexed with 553-49
分子名称: 553-49 VH, 553-49 VL, Spike protein S1
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2022-01-21
公開日2022-07-20
最終更新日2022-09-14
実験手法ELECTRON MICROSCOPY (4.06 Å)
主引用文献Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer.
J.Virol., 96, 2022
7WP0
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Cryo-EM structure of SARS-CoV-2 Delta S6P trimer in complex with neutralizing antibody VacW-209 (local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, IG c335_light_IGLV1-40_IGLJ3, Spike protein S1, ...
著者Zheng, Q, Sun, H, Ju, B, Zhang, Z, Li, S, Xia, N.
登録日2022-01-22
公開日2022-07-20
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.71 Å)
主引用文献Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209.
Cell Res., 32, 2022
7WP2
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Cryo-EM structure of SARS-CoV-2 C.1.2 S6P trimer in complex with neutralizing antibody VacW-209 (local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, VacW-209 heavy chain, ...
著者Zheng, Q, Sun, H, Ju, B, Zhang, Z, Li, S, Xia, N.
登録日2022-01-22
公開日2022-07-20
実験手法ELECTRON MICROSCOPY (3.52 Å)
主引用文献Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209.
Cell Res., 32, 2022
7WZ2
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SARS-CoV-2 (D614G) Spike trimer
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2022-02-16
公開日2022-07-20
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer.
J.Virol., 96, 2022
7XTZ
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BU of 7xtz by Molmil
Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-1 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, BILIVERDINE IX ALPHA, ...
著者Qu, K, Chen, Q, Ciazynska, K.A, Liu, B, Zhang, X, Wang, J, He, Y, Guan, J, He, J, Liu, T, Zhang, X, Carter, A.P, Xiong, X, Briggs, J.A.G.
登録日2022-05-18
公開日2022-07-20
最終更新日2022-08-17
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike.
Plos Pathog., 18, 2022
7XU1
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Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-122 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, BILIVERDINE IX ALPHA, ...
著者Qu, K, Chen, Q, Ciazynska, K.A, Liu, B, Zhang, X, Wang, J, He, Y, Guan, J, He, J, Liu, T, Zhang, X, Carter, A.P, Xiong, X, Briggs, J.A.G.
登録日2022-05-18
公開日2022-07-20
最終更新日2022-08-17
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike.
Plos Pathog., 18, 2022
7XU5
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BU of 7xu5 by Molmil
Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed 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, BILIVERDINE IX ALPHA, ...
著者Qu, K, Chen, Q, Ciazynska, K.A, Liu, B, Zhang, X, Wang, J, He, Y, Guan, J, He, J, Liu, T, Zhang, X, Carter, A.P, Xiong, X, Briggs, J.A.G.
登録日2022-05-18
公開日2022-07-20
最終更新日2022-08-17
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike.
Plos Pathog., 18, 2022
7XU6
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BU of 7xu6 by Molmil
Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), incubated in Low pH after 40-Day Storage in PBS, Locked-2 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, BILIVERDINE IX ALPHA, ...
著者Qu, K, Chen, Q, Ciazynska, K.A, Liu, B, Zhang, X, Wang, J, He, Y, Guan, J, He, J, Liu, T, Zhang, X, Carter, A.P, Xiong, X, Briggs, J.A.G.
登録日2022-05-18
公開日2022-07-20
最終更新日2022-08-17
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike.
Plos Pathog., 18, 2022
7P5G
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BU of 7p5g by Molmil
NMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506 fragment in HFIP/H2O
分子名称: Spike glycoprotein
著者Santoro, A, Buonocore, M, Grimaldi, M, D'Ursi, A.M.
登録日2021-07-14
公開日2022-07-27
最終更新日2024-06-19
実験手法SOLUTION NMR
主引用文献Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site.
Heliyon, 8, 2022
7P5Q
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NMR structure of a peptide deriving from SARS-CoV-2 Lineage B.1.1.7 S RBD 482-506 fragment in HFIP/H2O
分子名称: Spike glycoprotein
著者Santoro, A, Buonocore, M, Grimaldi, M, D'Ursi, A.M.
登録日2021-07-14
公開日2022-07-27
最終更新日2024-06-19
実験手法SOLUTION NMR
主引用文献Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site.
Heliyon, 8, 2022
7P5S
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BU of 7p5s by Molmil
NMR structure of a peptide deriving from SARS-CoV-2 Lineages P.1 and B.1.351 S RBD 482-506 fragment in HFIP/H2O
分子名称: Spike glycoprotein
著者Santoro, A, Buonocore, M, Grimaldi, M, D'Ursi, A.M.
登録日2021-07-14
公開日2022-07-27
最終更新日2024-06-19
実験手法SOLUTION NMR
主引用文献Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site.
Heliyon, 8, 2022
7S74
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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI38
分子名称: 3C-like proteinase, N-(tert-butylcarbamoyl)-3-methyl-L-valyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-L-leucinamide
著者Yang, K.S, Sankaran, B, Liu, W.R.
登録日2021-09-15
公開日2022-07-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240, 2022
7WZ1
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SARS-CoV-2 Omicron Spike trimer
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2022-02-16
公開日2022-07-27
最終更新日2022-09-14
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer.
J.Virol., 96, 2022
8D36
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BU of 8d36 by Molmil
Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody COV44-62
分子名称: Neutralizing antibody COV44-62 heavy chain, Neutralizing antibody COV44-62 light chain, Spike protein S2 fusion peptide
著者Yuan, M, Lee, C.C.D, Wilson, I.A.
登録日2022-05-31
公開日2022-07-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Broadly neutralizing antibodies target the coronavirus fusion peptide.
Science, 377, 2022
8D6Z
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Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV91-27
分子名称: Neutralizing antibody COV91-27 heavy chain, Neutralizing antibody COV91-27 light chain, Spike protein S2 fusion peptide
著者Lee, C.C.D, Lin, T.H, Yuan, M, Wilson, I.A.
登録日2022-06-06
公開日2022-07-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Broadly neutralizing antibodies target the coronavirus fusion peptide.
Science, 377, 2022
8DAO
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Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79
分子名称: COV44-79 heavy chain constant domain, COV44-79 heavy chain variable domain, COV44-79 light chain constant domain, ...
著者Lin, T.H, Lee, C.C.D, Yuan, M, Wilson, I.A.
登録日2022-06-13
公開日2022-07-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Broadly neutralizing antibodies target the coronavirus fusion peptide.
Science, 377, 2022
7FH0
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Crystallographic structure of two neutralizing nanobodies in complex with SARS-CoV-2 spike receptor-binding Domain (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, DI(HYDROXYETHYL)ETHER, ...
著者Zheng, P, Jin, J.
登録日2021-07-28
公開日2022-08-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Hetero-bivalent nanobodies provide broad-spectrum protection against SARS-CoV-2 variants of concern including Omicron.
Cell Res., 32, 2022

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