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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: 2020-03-11 (最終更新日: 4 weeks ago)2020-10-28
全エントリー (550)代表構造 (235)最新のエントリー (9)
7CT5
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S PROTEIN OF SARS-COV-2 IN COMPLEX BOUND WITH T-ACE2
分子名称:Spike glycoprotein, Angiotensin-converting enzyme 2, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Guo, L., Bi, W.W., Zhang, Y.Y., Yan, R.H., Li, Y.N., Zhou, Q., Dang, B.B.
登録日2020-08-18
公開日2020-11-18
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献Engineered Trimeric ACE2 Binds "Three-up" Spike Protein to Potently Inhibit SARS-CoVs and Mutants
To Be Published
7KOA
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ROOM TEMPERATURE STRUCTURE OF SARS-COV-2 NSP10/16 METHYLTRANSFERASE IN A COMPLEX WITH CAP-0 AND SAM DETERMINED BY PINK-BEAM SERIAL CRYSTALLOGRAPHY
分子名称:2'-O-methyltransferase, Non-structural protein 10, P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE, ...
著者Wilamowski, M., Sherrell, D.A., Minasov, G., Shuvalova, L., Lavens, A., Henning, R., Maltseva, N., Rosas-Lemus, M., Kim, Y., Satchell, K.J.F., Srajer, V., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-11-07
公開日2020-11-18
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography
To Be Published
7CDI
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CRYSTAL STRUCTURE OF SARS-COV-2 ANTIBODY P2C-1F11 WITH RBD
分子名称:Spike protein S1, antibody P2C-1F11 heavy chain, antibody P2C-1F11 light chain, ...
著者Wang, X., Zhang, L., Ge, J., Wang, R.
登録日2020-06-19
公開日2020-11-18
実験手法X-RAY DIFFRACTION (2.96 Å)
主引用文献Crystal structure of SARS-CoV-2 antibody P2C-1F11 and RBD
To be published
7KOK
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THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2, C111S MUTANT, IN COMPLEX WITH PLP_SNYDER496
分子名称:Papain-like protease, 5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ZINC ION, ...
著者Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-11-09
公開日2020-11-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder496
to be published
7KOL
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THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 IN COMPLEX WITH PLP_SNYDER496
分子名称:Papain-Like Protease, 5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ZINC ION, ...
著者Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-11-09
公開日2020-11-18
実験手法X-RAY DIFFRACTION (2.58 Å)
主引用文献The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder496
to be published
7KOJ
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THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2, C111S MUTANT, IN COMPLEX WITH PLP_SNYDER494
分子名称:Papain-like protease, 2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]-5-{[(prop-2-en-1-yl)carbamoyl]amino}benzamide, ZINC ION, ...
著者Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-11-09
公開日2020-11-18
実験手法X-RAY DIFFRACTION (2.02 Å)
主引用文献The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494
to be published
7CDJ
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CRYSTAL STRUCTURE OF SARS-COV-2 ANTIBODY P2C-1A3 WITH RBD
分子名称:Spike protein S1, antibody P2C-1A3 heavy chain, antibody P2C-1A3 light chain, ...
著者Wang, X., Zhang, L., Ge, J., Wang, R.
登録日2020-06-19
公開日2020-11-18
実験手法X-RAY DIFFRACTION (3.396 Å)
主引用文献Crystal structure of SARS-CoV-2 antibody P2C-1A3 and RBD
To Be Published
7KJR
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CRYO-EM STRUCTURE OF SARS-COV-2 ORF3A
分子名称:Protein 3a, Apolipoprotein A-I, 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
著者Kern, D.M., Hoel, C.M., Kotecha, A., Brohawn, S.G.
登録日2020-10-26
公開日2020-11-18
実験手法ELECTRON MICROSCOPY (2.08 Å)
主引用文献Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs.
Biorxiv, 2020
7KPH
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SARS-COV-2 MAIN PROTEASE IN MATURE FORM
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., Oliva, G., Godoy, A.S.
登録日2020-11-11
公開日2020-11-18
実験手法X-RAY DIFFRACTION (1.46 Å)
主引用文献SARS-CoV-2 Main Protease in mature form
To Be Published
7KKK
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SARS-COV-2 SPIKE IN COMPLEX WITH NEUTRALIZING NANOBODY NB6
分子名称:SARS-CoV-2 spike glycoprotein, Synthetic nanobody Nb6, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Schoof, M.S., Faust, B.F., Saunders, R.A., Sangwan, S., Rezelj, V., Hoppe, N., Boone, M., Billesboelle, C.B., Puchades, C., Azumaya, C.M., Kratochvil, H.T., Zimanyi, M., Desphande, I., Liang, J., Dickinson, S., Nguyen, H.C., Chio, C.M., Merz, G.E., Thompson, M.C., Diwanji, D., Schaefer, K., Anand, A.A., Dobzinski, N., Zha, B.S., Simoneau, C.R., Leon, K., White, K.M., Chio, U.S., Gupta, M., Jin, M., Li, F., Liu, Y., Zhang, K., Bulkley, D., Sun, M., Smith, A.M., Rizo, A.N., Moss, F., Brilot, A.F., Pourmal, S., Trenker, R., Pospiech, T., Gupta, S., Barsi-Rhyne, B., Belyy, V., Barile-Hill, A.W., Nock, S., Liu, Y., Krogan, N.J., Ralston, C.Y., Swaney, D.L., Garcia-Sastre, A., Ott, M., Vignuzzi, M., Walter, P., Manglik, A., QCRG Structural Biology Consortium
登録日2020-10-27
公開日2020-11-11
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike
Science, 2020
7D4F
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STRUCTURE OF COVID-19 RNA-DEPENDENT RNA POLYMERASE BOUND TO SURAMIN
分子名称:Non-structural protein 8, Non-structural protein 7, Non-structural protein 12, ...
著者Li, Z., Yin, W., Zhou, Z., Yu, X., Xu, H.
登録日2020-09-23
公開日2020-11-11
実験手法ELECTRON MICROSCOPY (2.57 Å)
主引用文献Structural basis for repurposing a 100-years-old drug suramin for treating COVID-19
To Be Published
7KL9
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STRUCTURE OF THE SARS-COV-2 S 6P TRIMER IN COMPLEX WITH THE ACE2 PROTEIN DECOY, CTC-445.2 (STATE 4)
分子名称:Spike glycoprotein, CTC-445.2 inhibitor, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Barnes, C.O., Bjorkman, P.J.
登録日2020-10-29
公開日2020-11-11
実験手法ELECTRON MICROSCOPY (4.1 Å)
主引用文献De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2
Science, 2020
7C33
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MACRO DOMAIN OF SARS-COV-2 IN COMPLEX WITH ADP-RIBOSE
分子名称:Macro domain from non-structural protein 3, ADENOSINE-5-DIPHOSPHORIBOSE
著者Lin, M.H., Hsu, C.H.
登録日2020-05-11
公開日2020-11-11
実験手法X-RAY DIFFRACTION (3.83 Å)
主引用文献Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain.
Acs Infect Dis., 2020
7CZ4
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STRUCTURE OF SARS-COV-2 MACRO DOMAIN IN COMPLEX WITH ADP-RIBOSE
分子名称:Macro domain from non-structural protein 3, ADENOSINE-5-DIPHOSPHORIBOSE
著者Lin, M.H., Hsu, C.H.
登録日2020-09-07
公開日2020-11-11
実験手法X-RAY DIFFRACTION (2.64 Å)
主引用文献Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain.
Acs Infect Dis., 2020
7KJ4
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SARS-COV-2 SPIKE GLYCOPROTEIN WITH THREE ACE2 BOUND
分子名称:Spike glycoprotein, Angiotensin-converting enzyme 2, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, J., Xiao, T.S., Cai, Y.F., Chen, B.
登録日2020-10-25
公開日2020-11-11
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro.
Biorxiv, 2020
7KJ2
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SARS-COV-2 SPIKE GLYCOPROTEIN WITH ONE ACE2 BOUND
分子名称:Spike glycoprotein, Angiotensin-converting enzyme 2, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, J., Xiao, T.S., Cai, Y.F., Chen, B.
登録日2020-10-25
公開日2020-11-11
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro.
Biorxiv, 2020
7KJ3
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SARS-COV-2 SPIKE GLYCOPROTEIN WITH TWO ACE2 BOUND
分子名称:Spike glycoprotein, Angiotensin-converting enzyme 2, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, J., Xiao, T.S., Cai, Y.F., Chen, B.
登録日2020-10-25
公開日2020-11-11
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro.
Biorxiv, 2020
7KJ5
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SARS-COV-2 SPIKE GLYCOPROTEIN, PREFUSION WITH ONE RBD UP CONFORMATION
分子名称:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
著者Zhang, J., Xiao, T.S., Cai, Y.F., Chen, B.
登録日2020-10-25
公開日2020-11-11
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro.
Biorxiv, 2020
7KKL
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SARS-COV-2 SPIKE IN COMPLEX WITH NEUTRALIZING NANOBODY MNB6
分子名称:SARS-CoV-2 spike glycoprotein, Synthetic nanobody mNb6, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Schoof, M.S., Faust, B.F., Saunders, R.A., Sangwan, S., Rezelj, V., Hoppe, N., Boone, M., Billesboelle, C.B., Puchades, C., Azumaya, C.M., Kratochvil, H.T., Zimanyi, M., Desphande, I., Liang, J., Dickinson, S., Nguyen, H.C., Chio, C.M., Merz, G.E., Thompson, M.C., Diwanji, D., Schaefer, K., Anand, A.A., Dobzinski, N., Zha, B.S., Simoneau, C.R., Leon, K., White, K.M., Chio, U.S., Gupta, M., Jin, M., Li, F., Liu, Y., Zhang, K., Bulkley, D., Sun, M., Smith, A.M., Rizo, A.N., Moss, F., Brilot, A.F., Pourmal, S., Trenker, R., Pospiech, T., Gupta, S., Barsi-Rhyne, B., Belyy, V., Barile-Hill, A.W., Nock, S., Liu, Y., Krogan, N.J., Ralston, C.Y., Swaney, D.L., Garcia-Sastre, A., Ott, M., Vignuzzi, M., Walter, P., Manglik, A., QCRG Structural Biology Consortium
登録日2020-10-27
公開日2020-11-11
実験手法ELECTRON MICROSCOPY (2.85 Å)
主引用文献An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike
Science, 2020
7CJF
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CRYSTAL STRUCTURE OF SARS-COV-2 RBD IN COMPLEX WITH A NEUTRALIZING ANTIBODY FAB
分子名称:antibody heavy chain, antibody light chain, Spike glycoprotein, ...
著者Guo, Y., Li, X., Zhang, G., Fu, D., Schweizer, L., Zhang, H., Rao, Z.
登録日2020-07-10
公開日2020-11-11
実験手法X-RAY DIFFRACTION (2.108 Å)
主引用文献Crystal structure of SARS-CoV-2 RBD in complex with an antibody Fab
To Be Published
7KE4
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SARS-COV-2 D614G 3 RBD DOWN SPIKE PROTEIN TRIMER WITHOUT THE P986-P987 STABILIZING MUTATIONS (S-GSAS-D614G SUB-CLASS)
分子名称:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
著者Gobeil, S., Acharya, P.
登録日2020-10-10
公開日2020-11-04
実験手法ELECTRON MICROSCOPY (3.21 Å)
主引用文献D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction.
Biorxiv, 2020
7D7T
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CRYSTAL STRUCTURE OF THE SARS-COV-2 PAPAIN-LIKE PROTEASE (PLPRO) C112S MUTANT BOUND TO COMPOUND S43
分子名称:papain-like protease, ZINC ION, N-[(3-acetamidophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide
著者Liu, J., Wang, Y., Xu, X., Pan, L.
登録日2020-10-05
公開日2020-11-04
実験手法X-RAY DIFFRACTION (3.15 Å)
主引用文献Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant
To Be Published
7KDL
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SARS-COV-2 D614G 1-RBD UP SPIKE PROTEIN TRIMER WITHOUT THE P986-P987 STABILIZING MUTATIONS (S-GSAS-D614G)
分子名称:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
著者Gobeil, S., Acharya, P.
登録日2020-10-08
公開日2020-11-04
実験手法ELECTRON MICROSCOPY (2.96 Å)
主引用文献D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction.
Biorxiv, 2020
7KE7
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SARS-COV-2 D614G 3-RBD-DOWN SPIKE PROTEIN TRIMER WITHOUT THE P986-P987 STABILIZING MUTATIONS (S-GSAS-D614G SUB-CLASSIFICATION)
分子名称:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
著者Gobeil, S., Acharya, P.
登録日2020-10-10
公開日2020-11-04
実験手法ELECTRON MICROSCOPY (3.32 Å)
主引用文献D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction.
Biorxiv, 2020
7ACS
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THE SARS-COV-2 NUCLEOCAPSID PHOSPHOPROTEIN N-TERMINAL DOMAIN IN COMPLEX WITH 7MER DSRNA
分子名称:Nucleoprotein, RNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3'), RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')
著者Veverka, V.
登録日2020-09-11
公開日2020-11-04
実験手法SOLUTION NMR
主引用文献The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 7mer ssRNA
To Be Published
171313
件を2020-11-18に公開中