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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
7N6N
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SARS-CoV-2 Main protease C145S mutant in complex with N and C-terminal residues
分子名称: 3C-like proteinase
著者Noske, G.D, Nakamura, A.M, Gawriljuk, V.O, Lima, G.M.A, Zeri, A.C.M, Nascimento, A.F.Z, Fernandes, R.S, Oliva, G, Godoy, A.S.
登録日2021-06-08
公開日2021-06-16
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.
J.Mol.Biol., 433, 2021
7NTK
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PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex
分子名称: 1,2-ETHANEDIOL, CITRATE ANION, Envelope small membrane protein, ...
著者Javorsky, A, Kvansakul, M.
登録日2021-03-10
公開日2021-06-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain.
Commun Biol, 4, 2021
7CUT
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BU of 7cut by Molmil
Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with Z-VAD-FMK
分子名称: 3C protein, DIMETHYL SULFOXIDE, GLYCEROL, ...
著者Lu, M, Yang, H.T, Wang, Z.Y, Zhao, Y, Xing, Y.F.
登録日2020-08-24
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.82 Å)
主引用文献Identification of proteasome and caspase inhibitors targeting SARS-CoV-2 M pro .
Signal Transduct Target Ther, 6, 2021
7CWT
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BU of 7cwt by Molmil
SARS-CoV-2 Spike protein in complex with hb27 and fc05 Fab cocktail
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain Fab of FC05, Heavy chain Fab of HB27, ...
著者Cui, Z, Wang, X.
登録日2020-08-31
公開日2021-06-23
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Structure-based development of human antibody cocktails against SARS-CoV-2.
Cell Res., 31, 2021
7E5Y
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Molecular basis for neutralizing antibody 2B11 targeting SARS-CoV-2 RBD
分子名称: 2B11 Fab Heavy chain, 2B11 Fab Light chain, Spike protein S1
著者Wu, H, Yu, F, Wang, Q.S, Zhou, H, Wang, W.W, Zhao, T, Pan, Y.B, Yang, X.M.
登録日2021-02-21
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.59 Å)
主引用文献Screening of potent neutralizing antibodies against SARS-CoV-2 using convalescent patients-derived phage-display libraries.
Cell Discov, 7, 2021
7EB5
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Cryo-EM structure of SARS-CoV-2 Spike D614G variant, two RBD-up conformation 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, Spike glycoprotein
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
登録日2021-03-08
公開日2021-06-23
最終更新日2022-01-05
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation.
J.Biol.Chem., 297, 2021
7EJ5
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Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-45
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, RBD-chAb45, ...
著者Yang, T.J, Yu, P.Y, Wu, H.C, Hsu, S.T.D.
登録日2021-04-01
公開日2021-06-23
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-45
To Be Published
7LC8
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SARS-CoV-2 spike Protein TM domain
分子名称: Spike protein S2'
著者Fu, Q, Chou, J.J.
登録日2021-01-10
公開日2021-06-23
最終更新日2024-05-15
実験手法SOLUTION NMR
主引用文献A Trimeric Hydrophobic Zipper Mediates the Intramembrane Assembly of SARS-CoV-2 Spike.
J.Am.Chem.Soc., 143, 2021
7M8S
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Crystal Structure of HLA-A*02:01 in complex with KLNDLCFTNV, an 10-mer epitope from SARS-CoV-2 Spike (S386-395)
分子名称: Beta-2-microglobulin, GLYCEROL, HLA class I histocompatibility antigen, ...
著者Gras, S, Nguyen, A.T, Szeto, C.
登録日2021-03-30
公開日2021-06-23
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules
Biophysica, 1, 2021
7M8T
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Crystal Structure of HLA-A*11:01 in complex with NSASFSTFK, an 9-mer epitope from SARS-CoV-2 spike (S370-378)
分子名称: Beta-2-microglobulin, CALCIUM ION, CHLORIDE ION, ...
著者Gras, S, Nguyen, A.T, Szeto, C.
登録日2021-03-30
公開日2021-06-23
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules
Biophysica, 1, 2021
7M8U
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Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from SARS-CoV-2 spike (S896-904)
分子名称: Beta-2-microglobulin, HLA class I histocompatibility antigen B, alpha chain, ...
著者Gras, S, Nguyen, A.T, Szeto, C.
登録日2021-03-30
公開日2021-06-23
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules
Biophysica, 1, 2021
7MGR
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BU of 7mgr by Molmil
SARS-CoV-2 main protease in complex with nsp8/9 substrate peptide
分子名称: 3C-like proteinase, ALA-VAL-LYS-LEU-GLN-ASN-ASN-GLU
著者MacDonald, E.A, Windsor, I.W, Hinshaw, S.M.
登録日2021-04-13
公開日2021-06-23
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.94 Å)
主引用文献Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease.
Acs Infect Dis., 7, 2021
7MGS
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BU of 7mgs by Molmil
SARS-CoV-2 main protease in complex with N-terminal autoprocessing substrate
分子名称: 3C-like proteinase, CHLORIDE ION, SER-ALA-VAL-LEU-GLN-SER-GLY-PHE
著者MacDonald, E.A, Windsor, I.W, Hinshaw, S.M.
登録日2021-04-13
公開日2021-06-23
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.84 Å)
主引用文献Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease.
Acs Infect Dis., 7, 2021
7N89
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Room-temperature X-ray structure of SARS-CoV-2 main protease C145A mutant in complex with substrate Ac-SAVLQSGF-CONH2
分子名称: 3C-like proteinase, ACE-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-NH2
著者Kovalevsky, A, Kneller, D.W, Coates, L.
登録日2021-06-14
公開日2021-06-23
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography.
Iucrj, 8, 2021
7L4Z
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BU of 7l4z by Molmil
Structure of SARS-CoV-2 spike RBD in complex with cyclic peptide
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, ACE-DTY-LYS-ALA-GLY-VAL-VAL-TYR-GLY-TYR-ASN-ALA-TRP-ILE-ARG-CYS-NH2, Spike protein S1
著者Christie, M, Mackay, J.P, Passioura, T, Payne, R.J.
登録日2020-12-21
公開日2021-06-30
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3.96 Å)
主引用文献Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display.
Acs Cent.Sci., 7, 2021
7AEG
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SARS-CoV-2 main protease in a covalent complex with SDZ 224015 derivative, compound 5
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE, N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide
著者Owen, C.D, Redhead, M.A, Lukacik, P, Strain-Damerell, C, Fearon, D, Brewitz, L, Collette, A, Robinson, C, Collins, P, Radoux, C, Navratilova, I, Douangamath, A, von Delft, F, Malla, T.R, Nugen, T, Hull, H, Tumber, A, Schofield, C.J, Hallet, D, Stuart, D.I, Hopkins, A.L, Walsh, M.A.
登録日2020-09-17
公開日2021-07-07
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19.
Sci Rep, 11, 2021
7EIN
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SARS-CoV-2 main proteinase complex with microbial metabolite leupeptin
分子名称: 3C-like proteinase, leupeptin
著者Fu, L.F, Feng, Y, Qi, J.X, Gao, G.F.
登録日2021-03-31
公開日2021-07-07
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Mechanism of Microbial Metabolite Leupeptin in the Treatment of COVID-19 by Traditional Chinese Medicine Herbs.
Mbio, 12, 2021
7N1T
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BU of 7n1t by Molmil
Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants
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, Cai, Y.F, Xiao, T.S, Rawson, S, Peng, H.Q, Sterling, S.M, Walsh Jr, R.M, Volloch, S.R, Chen, B.
登録日2021-05-28
公開日2021-07-07
最終更新日2021-08-18
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants.
Science, 373, 2021
7N1U
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Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants
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, Cai, Y.F, Xiao, T.S, Rawson, S, Peng, H.Q, Sterling, S.M, Walsh Jr, R.M, Volloch, S.R, Chen, B.
登録日2021-05-28
公開日2021-07-07
最終更新日2021-08-18
実験手法ELECTRON MICROSCOPY (3.14 Å)
主引用文献Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants.
Science, 373, 2021
7N3C
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BU of 7n3c by Molmil
Crystal Structure of Human Fab S24-202 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2
分子名称: 1,2-ETHANEDIOL, IODIDE ION, Nucleoprotein, ...
著者Kim, Y, Maltseva, N, Tesar, C, Jedrzejczak, R, Dugan, H, Stamper, C, Wilson, P, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2021-05-31
公開日2021-07-07
最終更新日2024-02-28
実験手法X-RAY DIFFRACTION (1.82 Å)
主引用文献Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
Iscience, 27, 2024
7N3D
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BU of 7n3d by Molmil
Crystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2
分子名称: 1,2-ETHANEDIOL, CHLORIDE ION, Nucleoprotein, ...
著者Kim, Y, Maltseva, N, Tesar, C, Jedrzejczak, R, Dugan, H, Stamper, C, Wilson, P, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2021-05-31
公開日2021-07-07
最終更新日2024-02-28
実験手法X-RAY DIFFRACTION (1.53 Å)
主引用文献Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
Iscience, 27, 2024
7OR9
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BU of 7or9 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and COVOX-278 Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, COVOX-222 Fab heavy chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-06-04
公開日2021-07-07
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.34 Å)
主引用文献Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.
Cell, 184, 2021
7ORA
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BU of 7ora by Molmil
Crystal structure of the T478K mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-45 and COVOX-253 Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, COVOX-253 Fab heavy chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-06-04
公開日2021-07-07
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.
Cell, 184, 2021
7ORB
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BU of 7orb by Molmil
Crystal structure of the L452R mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-75 and COVOX-253 Fabs
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-06-04
公開日2021-07-07
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.
Cell, 184, 2021
7R98
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Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody B6
分子名称: Nanobody B6, Nucleoprotein
著者Corbett, K.D, Ye, Q.
登録日2021-06-28
公開日2021-07-07
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.51 Å)
主引用文献Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies.
Front Immunol, 12, 2021

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