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COVID-19特辑

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冠状病毒
冠状病毒,2020. 由David S. Goodsell @ RCSB PDB原图修改

最近爆发的新型冠状病毒传染病(Novel Coronavirus disease 2019: COVID-19)对全世界的人们都构成了严重威胁。 为了尽早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以开发出有效的抗病毒药物,已经有很多科研人員开始了相关蛋白结构的研究,并且将所获得的结构数据存储于PDB。 PDBj为用户提供了COVID-19相关数据一览的门户页面,并将于每周三更新当日新发布的相关数据。

有关该病毒蛋白质的解说,请参见下面的“当月的分子”页面。

“所有结构”标签的页面则逐一罗列了所有的结构数据,包括由同一研究组提交的系列数据群。 “代表性结构”标签的页面精选具有相同氨基酸序列的结构数据中的高分辨率数据,不重复选择具同一氨基酸序列的数据,即使该数据可能包含不同配体。 “最新条目”标签内包含本周新更新数据。


Created: 2020-09-03 (last edited: more than 1 year ago)2020-12-02
7CHH
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BU of 7chh by Molmil
Cryo-EM structure of the SARS-CoV-2 S-6P in complex with BD-368-2 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BD-368-2 Fab heavy chain, ...
Authors:Xiao, J, Zhu, Q, Wang, G.
Deposit date:2020-07-05
Release date:2020-09-16
Last modified:2020-11-25
Method:ELECTRON MICROSCOPY (3.49 Å)
Cite:Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.
Cell, 183, 2020
6ZXN
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BU of 6zxn by Molmil
Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody Ty1, ...
Authors:Hallberg, B.M, Das, H.
Deposit date:2020-07-30
Release date:2020-09-23
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.
Nat Commun, 11, 2020
7AAP
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BU of 7aap by Molmil
Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP
Descriptor: MAGNESIUM ION, Non-structural protein 12, Non-structural protein 7, ...
Authors:Naydenova, K, Muir, K.W, Wu, L.F, Zhang, Z, Coscia, F, Peet, M, Castro-Hartman, P, Qian, P, Sader, K, Dent, K, Kimanius, D, Sutherland, J.D, Lowe, J, Barford, D, Russo, C.J.
Deposit date:2020-09-04
Release date:2020-09-23
Last modified:2023-04-19
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP.
Proc.Natl.Acad.Sci.USA, 118, 2021
7CAI
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BU of 7cai by Molmil
SARS-CoV-2 S trimer with two RBDs in the open state and complexed with two H014 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H014 Fab, ...
Authors:Zhe, L, Cao, L, Deng, Y, Sun, Y, Wang, N, Xie, L, Wang, Y, Rao, Z, Qin, C, Wang, X.
Deposit date:2020-06-08
Release date:2020-09-23
Last modified:2020-09-30
Method:ELECTRON MICROSCOPY (3.49 Å)
Cite:Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody.
Science, 369, 2020
7JKV
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BU of 7jkv by Molmil
Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420
Descriptor: 3C-like proteinase, N-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, PENTAETHYLENE GLYCOL
Authors:Bulut, H, Hattori, S.I, Das, D, Murayama, K, Mitsuya, H.
Deposit date:2020-07-29
Release date:2020-09-23
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication.
Nat Commun, 12, 2021
7JX6
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BU of 7jx6 by Molmil
STRUCTURE OF THE SARS-CoV-2 ORF8 ENCODED ACCESSORY PROTEIN
Descriptor: ORF8 protein, SODIUM ION
Authors:Hall, P.D, Nelson, C.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-08-26
Release date:2020-09-23
Method:X-RAY DIFFRACTION (1.61 Å)
Cite:Crystal Structure of the SARS-CoV-2 ORF8 Protein
To Be Published
7JZL
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BU of 7jzl by Molmil
SARS-CoV-2 spike in complex with LCB1 (2RBDs open)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, LCB1, ...
Authors:Park, Y.J, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-02
Release date:2020-09-23
Last modified:2020-11-04
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:De novo design of picomolar SARS-CoV-2 miniprotein inhibitors.
Science, 370, 2020
7JZM
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BU of 7jzm by Molmil
SARS-CoV-2 spike in complex with LCB3 (local refinement of the RBD and LCB3)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, LCB3, Spike glycoprotein
Authors:Park, Y.J, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-02
Release date:2020-09-23
Last modified:2020-11-04
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:De novo design of picomolar SARS-CoV-2 miniprotein inhibitors.
Science, 370, 2020
7JZN
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BU of 7jzn by Molmil
SARS-CoV-2 spike in complex with LCB3 (2RBDs open)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, LCB3, ...
Authors:Park, Y.J, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-02
Release date:2020-09-23
Last modified:2020-11-04
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:De novo design of picomolar SARS-CoV-2 miniprotein inhibitors.
Science, 370, 2020
7JZU
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BU of 7jzu by Molmil
SARS-CoV-2 spike in complex with LCB1 (local refinement of the RBD and LCB1)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, LCB1, Spike glycoprotein
Authors:Park, Y.J, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-02
Release date:2020-09-23
Last modified:2020-11-04
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:De novo design of picomolar SARS-CoV-2 miniprotein inhibitors.
Science, 370, 2020
5RL9
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BU of 5rl9 by Molmil
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1703168683
Descriptor: 1-(3-fluoro-4-methylphenyl)methanesulfonamide, Helicase, PHOSPHATE ION, ...
Authors:Newman, J.A, Yosaatmadja, Y, Douangamath, A, Aimon, A, Powell, A.J, Dias, A, Fearon, D, Dunnett, L, Brandao-Neto, J, Krojer, T, Skyner, R, Gorrie-Stone, T, Thompson, W, von Delft, F, Arrowsmith, C.H, Edwards, A, Bountra, C, Gileadi, O.
Deposit date:2020-09-16
Release date:2020-09-30
Last modified:2022-09-07
Method:X-RAY DIFFRACTION (1.788 Å)
Cite:Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Nat Commun, 12, 2021
7CWC
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BU of 7cwc by Molmil
Ambient-Temperature Serial Femtosecond X-ray Crystal structure of SARS-CoV-2 Main Protease at 2.1 A Resolution (P212121)
Descriptor: 3C-like proteinase
Authors:DeMirci, H.
Deposit date:2020-08-27
Release date:2020-09-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.
Structure, 29, 2021
7K3N
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BU of 7k3n by Molmil
Crystal Structure of NSP1 from SARS-CoV-2
Descriptor: Host translation inhibitor nsp1
Authors:Semper, C, Watanabe, N, Chang, C, Savchenko, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-09-11
Release date:2020-09-30
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Structural characterization of nonstructural protein 1 from SARS-CoV-2.
Iscience, 24, 2021
7K7P
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BU of 7k7p by Molmil
Structure of SARS-CoV-2 nonstuctural protein 1
Descriptor: Host translation inhibitor nsp1
Authors:Green, T.J, Petit, C.M, Clark, L.K.
Deposit date:2020-09-23
Release date:2020-09-30
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Structure of Nonstructural Protein 1 from SARS-CoV-2.
J.Virol., 95, 2021
7D47
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BU of 7d47 by Molmil
Crystal structure of SARS-CoV-2 Papain-like protease C111S
Descriptor: CALCIUM ION, Non-structural protein 3, ZINC ION
Authors:Wu, K.-P, Chen, S.-K, Lu, Y.-C, Huang, Y.-C.J, Lee, M.-H.
Deposit date:2020-09-22
Release date:2020-10-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.97 Å)
Cite:Crystal structure of SARS-CoV-2 Papain-like protease
To Be Published
7JOY
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BU of 7joy by Molmil
Product structure of SARS-CoV-2 Mpro C145A mutant in complex with its C-terminal autoprocessing sequence.
Descriptor: 3C-like proteinase
Authors:Lee, J, Worrall, L.J, Paetzel, M, Strynadka, N.C.J.
Deposit date:2020-08-07
Release date:2020-10-07
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.
Nat Commun, 11, 2020
7JWB
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BU of 7jwb by Molmil
SARS CoV2 Spike ectodomain with engineered trimerized VH binder
Descriptor: Spike glycoprotein, autonomous human heavy chain variable domain
Authors:QCRG Structural Biology Consortium
Deposit date:2020-08-25
Release date:2020-10-07
Last modified:2020-12-30
Method:ELECTRON MICROSCOPY (6 Å)
Cite:Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2.
Nat.Chem.Biol., 17, 2021
7K43
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BU of 7k43 by Molmil
SARS-CoV-2 spike in complex with the S2M11 neutralizing antibody Fab fragment
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2M11 Fab fragment (heavy chain), ...
Authors:Tortorici, M.A, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-14
Release date:2020-10-07
Last modified:2021-01-27
Method:ELECTRON MICROSCOPY (2.6 Å)
Cite:Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.
Science, 370, 2020
7K45
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BU of 7k45 by Molmil
SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment (local refinement of the RBD and Fab variable domains)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2E12 neutralizing antibody Fab fragment (heavy chain), S2E12 neutralizing antibody Fab fragment (light chain), ...
Authors:Tortorici, M.A, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-14
Release date:2020-10-07
Last modified:2023-10-18
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.
Science, 370, 2020
7K4N
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BU of 7k4n by Molmil
SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2E12 neutralizing antibody Fab fragment (heavy chain), ...
Authors:Tortorici, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-15
Release date:2020-10-07
Last modified:2020-12-02
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.
Science, 370, 2020
6XKP
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BU of 6xkp by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-270
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CV07-270 Heavy Chain, CV07-270 Light Chain, ...
Authors:Liu, H, Yuan, M, Zhu, X, Wu, N.C, Wilson, I.A.
Deposit date:2020-06-26
Release date:2020-10-14
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.72 Å)
Cite:A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.
Cell, 183, 2020
6XKQ
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BU of 6xkq by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-250
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CV07-250 Heavy Chain, CV07-250 Light Chain, ...
Authors:Yuan, M, Liu, H, Zhu, X, Wu, N.C, Wilson, I.A.
Deposit date:2020-06-26
Release date:2020-10-14
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.
Cell, 183, 2020
6ZPE
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BU of 6zpe by Molmil
Nonstructural protein 10 (nsp10) from SARS CoV-2
Descriptor: CHLORIDE ION, GLYCEROL, Replicase polyprotein 1ab, ...
Authors:Fisher, S.Z, Kozielski, F.
Deposit date:2020-07-08
Release date:2020-10-14
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2.
Int J Mol Sci, 21, 2020
7JMW
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BU of 7jmw by Molmil
Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with cross-neutralizing antibody COVA1-16 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, COVA1-16 heavy chain, COVA1-16 light chain, ...
Authors:Liu, H, Yuan, M, Zhu, X, Wu, N.C, Wilson, I.A.
Deposit date:2020-08-03
Release date:2020-10-14
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.89 Å)
Cite:Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity.
Immunity, 53, 2020
7JV2
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BU of 7jv2 by Molmil
SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody Fab fragment (local refinement of the receptor-binding motif and Fab variable domains)
Descriptor: S2H13 Fab heavy chain, S2H13 Fab light chain, Spike glycoprotein
Authors:Park, Y.J, Tortorici, M.A, Walls, A.C, Czudnochowski, N, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Snell, G, Veesler, D.
Deposit date:2020-08-20
Release date:2020-10-14
Last modified:2021-01-27
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
Cell, 183, 2020

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数据于2024-05-01公开中

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