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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
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
7BNN
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Open conformation of D614G SARS-CoV-2 spike with 1 Erect 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
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 (3.5 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
7BNO
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BU of 7bno by Molmil
Open conformation of D614G SARS-CoV-2 spike with 2 Erect RBDs
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 (4.2 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
7KGJ
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BU of 7kgj by Molmil
Crystal structure of synthetic nanobody (Sb45) complexes with SARS-CoV-2 receptor binding domain
分子名称: Sb45, Sybody-45, Synthetic Nanobody, ...
著者Jiang, J, Ahmad, J, Natarajan, K, Boyd, L.F, Margulies, D.H.
登録日2020-10-16
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
J.Biol.Chem., 297, 2021
7KGK
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BU of 7kgk by Molmil
Crystal structure of synthetic nanobody (Sb16) complexes with SARS-CoV-2 receptor binding domain
分子名称: Sb16, Sybody-16, Synthetic Nanobody, ...
著者Jiang, J, Ahmad, J, Natarajan, K, Boyd, L.F, Margulies, D.H.
登録日2020-10-16
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
J.Biol.Chem., 297, 2021
7KLW
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BU of 7klw by Molmil
Crystal structure of synthetic nanobody (Sb45+Sb68) complexes with SARS-CoV-2 receptor binding domain
分子名称: SB45, Synthetic Nanobody, SB68, ...
著者Jiang, J, Ahmad, J, Natarajan, K, Boyd, L.F, Margulies, D.H.
登録日2020-11-01
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
J.Biol.Chem., 297, 2021
7KXJ
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BU of 7kxj by Molmil
SARS-CoV-2 spike protein in complex with Fab 15033-7, 3-"up", asymmetric
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, Fab 15033-7 heavy chain, ...
著者Li, Z, Rini, J.
登録日2020-12-04
公開日2021-02-03
最終更新日2021-08-25
実験手法ELECTRON MICROSCOPY (6.4 Å)
主引用文献Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
J.Mol.Biol., 433, 2021
7KXK
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BU of 7kxk by Molmil
SARS-CoV-2 spike protein in complex with Fab 15033-7, 2-"up"-1-"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, Fab 15033-7 heavy chain, ...
著者Li, Z, Rini, J.
登録日2020-12-04
公開日2021-02-03
最終更新日2021-08-25
実験手法ELECTRON MICROSCOPY (5 Å)
主引用文献Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
J.Mol.Biol., 433, 2021
7KZB
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BU of 7kzb by Molmil
Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1antibodies
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, Fab heavy chain of CR3014-C8 antibody, ...
著者Langley, D.B, Christ, D.
登録日2020-12-10
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.83 Å)
主引用文献Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1 antibodies.
Mabs, 13
7L3N
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BU of 7l3n by Molmil
SARS-CoV 2 Spike Protein bound to LY-CoV555
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, LY-CoV555 Fab heavy chain, ...
著者Goldsmith, J.A, McLellan, J.S.
登録日2020-12-18
公開日2021-02-03
実験手法ELECTRON MICROSCOPY (3.27 Å)
主引用文献LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection.
Biorxiv, 2020
7LFE
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BU of 7lfe by Molmil
SARS-CoV-2 Main protease immature form - F2X Entry Library E03 fragment
分子名称: (2R,4R)-1-phenylhexahydropyrimidine-2,4-diol, 3C-like proteinase, DI(HYDROXYETHYL)ETHER, ...
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2021-01-16
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.79 Å)
主引用文献A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.
J.Mol.Biol., 433, 2021
7LFP
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BU of 7lfp by Molmil
SARS-CoV-2 Main protease immature form - F2X Entry Library G05 fragment
分子名称: 3C-like proteinase, DI(HYDROXYETHYL)ETHER, DIMETHYL SULFOXIDE, ...
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2021-01-18
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.
J.Mol.Biol., 433, 2021
7LFZ
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BU of 7lfz by Molmil
Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope IPRRNVATL
分子名称: Beta-2-microglobulin, HLA class I histocompatibility antigen, B-7 alpha chain, ...
著者Patskovska, L, Patskovsky, Y, Krogsgaard, M.
登録日2021-01-19
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope IPRRNVATL
To Be Published
7LG0
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BU of 7lg0 by Molmil
Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL
分子名称: Beta-2-microglobulin, HEXAETHYLENE GLYCOL, HLA class I histocompatibility antigen, ...
著者Patskovska, L, Patskovsky, Y, Krogsgaard, M.
登録日2021-01-19
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL
To Be Published
7LG2
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BU of 7lg2 by Molmil
Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope ALWEIQQVV
分子名称: Beta-2-microglobulin, GLYCEROL, MHC class I antigen, ...
著者Patskovska, L, Patskovsky, Y, Krogsgaard, M.
登録日2021-01-19
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope ALWEIQQVV
To Be Published
7LG3
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BU of 7lg3 by Molmil
Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope KLWAQCVQL
分子名称: Beta-2-microglobulin, GLYCEROL, MHC class I antigen, ...
著者Patskovska, L, Patskovsky, Y, Krogsgaard, M.
登録日2021-01-19
公開日2021-02-03
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope KLWAQCVQL
To Be Published
7B17
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BU of 7b17 by Molmil
SARS-CoV-spike RBD bound to two neutralising nanobodies.
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 neutralizing biparatopic nanobody VE,nanobody E from Lama glama,SARS-CoV-2 neutralizing biparatopic nanobody VE,nanobody E from Lama glama, Spike protein S1
著者Hallberg, B.M, Das, H.
登録日2020-11-23
公開日2021-02-10
最終更新日2022-12-21
実験手法ELECTRON MICROSCOPY (4.01 Å)
主引用文献Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape
Science, 371, 2021
7KLG
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BU of 7klg by Molmil
SARS-CoV-2 RBD in complex with Fab 15033
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab 15033 heavy chain, Fab 15033 light chain, ...
著者Li, Z, Rini, J.M.
登録日2020-10-30
公開日2021-02-10
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
J.Mol.Biol., 433, 2021
7KLH
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BU of 7klh by Molmil
SARS-CoV-2 RBD in complex with Fab 15033-7
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab 15033-7 heavy chain, Fab 15033-7 light chain, ...
著者Li, Z, Rini, J.M.
登録日2020-10-30
公開日2021-02-10
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
J.Mol.Biol., 433, 2021
7KMK
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BU of 7kmk by Molmil
cryo-EM structure of SARS-CoV-2 spike in complex with Fab 15033-7, two RBDs bound
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, Fab 15033-7 heavy chain, ...
著者Li, Z, Rini, J.M.
登録日2020-11-03
公開日2021-02-10
最終更新日2021-08-25
実験手法ELECTRON MICROSCOPY (4.2 Å)
主引用文献Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
J.Mol.Biol., 433, 2021
7KML
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BU of 7kml by Molmil
cryo-EM structure of SARS-CoV-2 spike in complex with Fab 15033-7, three RBDs bound
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, Fab 15033-7 heavy chain, ...
著者Li, Z, Rini, J.M.
登録日2020-11-03
公開日2021-02-10
最終更新日2021-08-25
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
J.Mol.Biol., 433, 2021
7KS9
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BU of 7ks9 by Molmil
Cryo-EM structure of prefusion SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab
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, 910-30 Fab heavy chain, ...
著者Cerutti, G, Shapiro, L.
登録日2020-11-21
公開日2021-02-10
最終更新日2022-11-09
実験手法ELECTRON MICROSCOPY (4.75 Å)
主引用文献Paired heavy- and light-chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses.
Cell Rep, 37, 2021
7L0D
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BU of 7l0d by Molmil
SARS-CoV-2 Main Protease (Mpro) in Complex with ML188
分子名称: 3C-like proteinase, N-[(1R)-2-(tert-butylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-N-(4-tert-butylphenyl)furan-2-carboxamide
著者Lockbaum, G.J, Lee, J.M, Reyes, A.C, Nalivaika, E.A, Ali, A, Yilmaz, N.K, Thompson, P.R, Schiffer, C.A.
登録日2020-12-11
公開日2021-02-10
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.39 Å)
主引用文献Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188.
Viruses, 13, 2021
7L1F
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BU of 7l1f by Molmil
SARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate
分子名称: Non-structural protein 7, Non-structural protein 8, RNA (5'-R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3'), ...
著者Bravo, J.P.K, Taylor, D.W.
登録日2020-12-14
公開日2021-02-10
最終更新日2024-03-06
実験手法ELECTRON MICROSCOPY (3.89 Å)
主引用文献Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication.
Mol.Cell, 81, 2021
7L2C
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BU of 7l2c by Molmil
Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD)
分子名称: 2-51 heavy chain, 2-51 light chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Cerutti, G, Reddem, E.R, Shapiro, L.
登録日2020-12-16
公開日2021-02-10
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3.65 Å)
主引用文献Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.
Cell Host Microbe, 29, 2021

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