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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
7B3D
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BU of 7b3d by Molmil
Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with AMP at position -4 (structure 3)
分子名称: RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3'), RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3'), SARS-CoV-2 RNA-dependent RNA polymerase nsp12, ...
著者Kokic, G, Hillen, H.S, Tegunov, D, Dienemann, C, Seitz, F, Schmitzova, J, Farnung, L, Siewert, A, Hoebartner, C, Cramer, P.
登録日2020-11-30
公開日2020-12-23
最終更新日2024-05-01
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Mechanism of SARS-CoV-2 polymerase stalling by remdesivir.
Nat Commun, 12, 2021
7DMU
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BU of 7dmu by Molmil
Structure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39
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, Angiotensin-converting enzyme 2, ...
著者Arimori, T, Takagi, J.
登録日2020-12-07
公開日2020-12-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2.
Nat Commun, 12, 2021
7L09
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BU of 7l09 by Molmil
Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound domain-swapped antibody 2G12 from masked 3D refinement
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, 2G12 heavy chain, ...
著者Manne, K, Henderson, R, Acharya, P.
登録日2020-12-11
公開日2020-12-30
最終更新日2021-06-09
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.
Cell, 184, 2021
7L6T
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BU of 7l6t by Molmil
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.
分子名称: 2'-O-methyltransferase, CHLORIDE ION, FORMIC ACID, ...
著者Minasov, G, Shuvalova, L, Rosas-Lemus, M, Kiryukhina, O, Brunzelle, J.S, Satchell, K.J.F, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-12-23
公開日2021-01-06
最終更新日2024-03-06
実験手法X-RAY DIFFRACTION (1.78 Å)
主引用文献Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16.
Sci.Signal., 14, 2021
7BF4
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BU of 7bf4 by Molmil
Crystal structure of SARS-CoV-2 macrodomain in complex with GMP
分子名称: 1,2-ETHANEDIOL, GUANOSINE-5'-MONOPHOSPHATE, NSP3 macrodomain
著者Ni, X, Knapp, S, Chaikuad, A, Structural Genomics Consortium, Structural Genomics Consortium (SGC)
登録日2020-12-31
公開日2021-01-13
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.
Acs Med.Chem.Lett., 12, 2021
7CM4
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BU of 7cm4 by Molmil
Crystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59
分子名称: 1,2-ETHANEDIOL, IgG heavy chain, IgG light chain, ...
著者Kim, Y.G, Jeong, J.H, Bae, J.S, Lee, J.
登録日2020-07-24
公開日2021-01-20
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.71 Å)
主引用文献A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein.
Nat Commun, 12, 2021
7KGO
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BU of 7kgo by Molmil
Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N351-359
分子名称: Beta-2-microglobulin, CADMIUM ION, CHLORIDE ION, ...
著者Szeto, C, Chatzileontiadou, D.S.M, Riboldi-Tunnicliffe, A, Gras, S.
登録日2020-10-18
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.15 Å)
主引用文献The presentation of SARS-CoV-2 peptides by the common HLA-A * 02:01 molecule.
Iscience, 24, 2021
7KGP
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BU of 7kgp by Molmil
Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N316-324
分子名称: ACETATE ION, Beta-2-microglobulin, CADMIUM ION, ...
著者Szeto, C, Chatzileontiadou, D.S.M, Riboldi-Tunnicliffe, A, Gras, S.
登録日2020-10-18
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.396 Å)
主引用文献The presentation of SARS-CoV-2 peptides by the common HLA-A * 02:01 molecule.
Iscience, 24, 2021
7KGQ
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BU of 7kgq by Molmil
Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N222-230
分子名称: 1,2-ETHANEDIOL, Beta-2-microglobulin, CADMIUM ION, ...
著者Szeto, C, Chatzileontiadou, D.S.M, Riboldi-Tunnicliffe, A, Gras, S.
登録日2020-10-18
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.34 Å)
主引用文献The presentation of SARS-CoV-2 peptides by the common HLA-A * 02:01 molecule.
Iscience, 24, 2021
7KGR
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BU of 7kgr by Molmil
Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N159-167
分子名称: Beta-2-microglobulin, MHC class I antigen, Nucleoprotein
著者Szeto, C, Chatzileontiadou, D.S.M, Riboldi-Tunnicliffe, A, Gras, S.
登録日2020-10-18
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献The presentation of SARS-CoV-2 peptides by the common HLA-A * 02:01 molecule.
Iscience, 24, 2021
7KGS
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BU of 7kgs by Molmil
Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N138-146
分子名称: ACETATE ION, Beta-2-microglobulin, CADMIUM ION, ...
著者Szeto, C, Chatzileontiadou, D.S.M, Riboldi-Tunnicliffe, A, Gras, S.
登録日2020-10-18
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.58 Å)
主引用文献The presentation of SARS-CoV-2 peptides by the common HLA-A*02:01 molecule.
Iscience, 24, 2021
7KGT
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BU of 7kgt by Molmil
Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234
分子名称: ACETATE ION, Beta-2-microglobulin, CADMIUM ION, ...
著者Szeto, C, Chatzileontiadou, D.S.M, Riboldi-Tunnicliffe, A, Gras, S.
登録日2020-10-18
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献The presentation of SARS-CoV-2 peptides by the common HLA-A*02:01 molecule.
Iscience, 24, 2021
7KN5
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BU of 7kn5 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U
分子名称: 1,2-ETHANEDIOL, 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Liu, H, Yuan, M, Zhu, X, Wu, N.C, Wilson, I.A.
登録日2020-11-04
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.87 Å)
主引用文献Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.
Science, 371, 2021
7KN6
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BU of 7kn6 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
著者Liu, H, Yuan, M, Zhu, X, Wu, N.C, Wilson, I.A.
登録日2020-11-04
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.55 Å)
主引用文献Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.
Science, 371, 2021
7KN7
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BU of 7kn7 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
著者Liu, H, Yuan, M, Zhu, X, Wu, N.C, Wilson, I.A.
登録日2020-11-04
公開日2021-01-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.73 Å)
主引用文献Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.
Science, 371, 2021
7KSG
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BU of 7ksg by Molmil
SARS-CoV-2 spike in complex with nanobodies E
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody against SARS-CoV-2 glycoprotein, Spike glycoprotein
著者Hallberg, B.M, Das, H.
登録日2020-11-22
公開日2021-01-20
最終更新日2021-06-30
実験手法ELECTRON MICROSCOPY (3.33 Å)
主引用文献Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.
Science, 371, 2021
7C8J
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BU of 7c8j by Molmil
Structural basis for cross-species recognition of COVID-19 virus spike receptor binding domain to bat ACE2
分子名称: Angiotensin-converting enzyme, SARS-CoV-2 Receptor binding domain, ZINC ION
著者Liu, K.F, Wang, J, Tan, S.G, Niu, S, Wu, L.L, Zhang, Y.F, Pan, X.Q, Meng, Y.M, Chen, Q, Wang, Q.H, Wang, H.W, Qi, J.X, Gao, G.F.
登録日2020-06-01
公開日2021-01-27
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.18 Å)
主引用文献Cross-species recognition of SARS-CoV-2 to bat ACE2.
Proc.Natl.Acad.Sci.USA, 118, 2021
7DE1
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BU of 7de1 by Molmil
Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal RNA binding domain
分子名称: DI(HYDROXYETHYL)ETHER, Nucleoprotein
著者Chen, S, Kang, S.
登録日2020-11-01
公開日2021-01-27
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Structural Insight Into the SARS-CoV-2 Nucleocapsid Protein C-Terminal Domain Reveals a Novel Recognition Mechanism for Viral Transcriptional Regulatory Sequences.
Front Chem, 8, 2020
7KMG
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BU of 7kmg by Molmil
LY-CoV555 neutralizing antibody against SARS-CoV-2
分子名称: GLYCEROL, LY-CoV555 Fab heavy chain, LY-CoV555 Fab light chain, ...
著者Hendle, J, Pustilnik, A, Sauder, J.M, Coleman, K.A, Boyles, J.S, Dickinson, C.D.
登録日2020-11-02
公開日2021-01-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.16 Å)
主引用文献The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates.
Sci Transl Med, 13, 2021
7KMH
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BU of 7kmh by Molmil
LY-CoV488 neutralizing antibody against SARS-CoV-2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, LY-CoV488 Fab heavy chain, ...
著者Hendle, J, Pustilnik, A, Sauder, J.M, Boyles, J.S, Dickinson, C.D, Coleman, K.A.
登録日2020-11-02
公開日2021-01-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.72 Å)
主引用文献The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates.
Sci Transl Med, 13, 2021
7KMI
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BU of 7kmi by Molmil
LY-CoV481 neutralizing antibody against SARS-CoV-2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, LY-CoV481 Fab heavy chain, ...
著者Hendle, J, Pustilnik, A, Sauder, J.M, Coleman, K.A, Boyles, J.S, Dickinson, C.D.
登録日2020-11-02
公開日2021-01-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.73 Å)
主引用文献The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates.
Sci Transl Med, 13, 2021
7LCN
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BU of 7lcn by Molmil
Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1050.1
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, DH1050.1 heavy chain, ...
著者Manne, K, Acharya, P.
登録日2021-01-11
公開日2021-01-27
最終更新日2021-08-18
実験手法ELECTRON MICROSCOPY (3.35 Å)
主引用文献In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies.
Cell, 184, 2021
7LD1
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BU of 7ld1 by Molmil
Structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1047
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, DH1047 heavy chain, ...
著者Manne, K, Acharya, P.
登録日2021-01-12
公開日2021-01-27
最終更新日2021-08-18
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies.
Cell, 184, 2021
7LGO
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BU of 7lgo by Molmil
Crystal structure of the nucleic acid binding domain (NAB) of Nsp3 from SARS-CoV-2
分子名称: Non-structural protein 3
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2021-01-20
公開日2021-01-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.45 Å)
主引用文献Crystal structure of the nucleic acid binding domain (NAB) of Nsp3 from SARS-CoV-2
To Be Published
7BNM
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BU of 7bnm by Molmil
Closed conformation of D614G SARS-CoV-2 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, Spike glycoprotein
著者Benton, D.J, Wrobel, A.G, Rosenthal, P.B, Gamblin, S.J.
登録日2021-01-22
公開日2021-02-03
最終更新日2021-03-10
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 118, 2021

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