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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
所有结构 (4418)代表性结构 (1953)最新条目 (11)
8FEZ
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BU of 8fez by Molmil
Prefusion-stabilized SARS-CoV-2 spike protein
Descriptor: Spike glycoprotein
Authors:Gonzalez, K.J, Mousa, J.J, Strauch, E.M.
Deposit date:2022-12-07
Release date:2023-04-12
Method:ELECTRON MICROSCOPY (3.72 Å)
Cite:A general computational design strategy for stabilizing viral class I fusion proteins.
Biorxiv, 2023
8GZZ
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BU of 8gzz by Molmil
Local refinement of SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab
Descriptor: Spike protein S1, rabbit monoclonal antibody 1H1 Fab heavy chain, rabbit monoclonal antibody 1H1 Fab light chain
Authors:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-09-27
Release date:2023-04-12
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (3.52 Å)
Cite:Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants.
Commun Biol, 6, 2023
8H00
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BU of 8h00 by Molmil
SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab in the class 1 conformation
Descriptor: 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, ...
Authors:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-09-27
Release date:2023-04-12
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (3.41 Å)
Cite:Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants.
Commun Biol, 6, 2023
7WN2
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BU of 7wn2 by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab Heavy chain, Fab Light chain, ...
Authors:Yamamoto, A, Higashiura, A.
Deposit date:2022-01-17
Release date:2023-04-19
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol, 6, 2023
7WNB
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BU of 7wnb by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab Heavy chain, Fab Light chain, ...
Authors:Yamamoto, A, Higashiura, A.
Deposit date:2022-01-18
Release date:2023-04-19
Method:X-RAY DIFFRACTION (2.18 Å)
Cite:Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol, 6, 2023
7XJ6
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BU of 7xj6 by Molmil
SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 1 conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 55A8 heavy chain, ...
Authors:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-04-15
Release date:2023-04-19
Method:ELECTRON MICROSCOPY (3.29 Å)
Cite:SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 1 conformation
To Be Published
7XJ8
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BU of 7xj8 by Molmil
SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 2 conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 55A8 heavy chain, ...
Authors:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-04-15
Release date:2023-04-19
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 2 conformation
To Be Published
7XJ9
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BU of 7xj9 by Molmil
Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab
Descriptor: 55A8 heavy chain, 55A8 light chain, 58G6 heavy chain, ...
Authors:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-04-15
Release date:2023-04-19
Method:ELECTRON MICROSCOPY (3.27 Å)
Cite:Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab
To Be Published
7YOW
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BU of 7yow by Molmil
Crystal structure of SARS-CoV-2 omicron variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab
Descriptor: Fab Heavy chain, Fab Light chain, SULFATE ION, ...
Authors:Yamamoto, A, Higashiura, A.
Deposit date:2022-08-02
Release date:2023-04-19
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol, 6, 2023
7ZJL
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BU of 7zjl by Molmil
Delta SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue.
Descriptor: REGN10987 Fab homologue (Heavy chain), REGN10987 Fab homologue (Light chain), Spike glycoprotein
Authors:Pichkur, E.B, Lyukmanova, E.N, Shenkarev, Z.O.
Deposit date:2022-04-11
Release date:2023-04-19
Method:ELECTRON MICROSCOPY (2.6 Å)
Cite:Delta SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue.
To Be Published
8C1V
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BU of 8c1v by Molmil
SARS-CoV-2 S-trimer (3 RBDs up) bound to TriSb92, fitted into cryo-EM map
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Sb92, ...
Authors:Huiskonen, J.T, Rissanen, I, Hannula, L.
Deposit date:2022-12-21
Release date:2023-04-19
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants.
Nat Commun, 14, 2023
8HEF
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BU of 8hef by Molmil
The Crystal structure of deuterated S-217622 (Ensitrelvir) bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor: 3C-like proteinase, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, GLYCEROL
Authors:Yan, M, Zhang, H.
Deposit date:2022-11-08
Release date:2023-04-19
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (1.51 Å)
Cite:Synthesis of deuterated S-217622 (Ensitrelvir) with antiviral activity against coronaviruses including SARS-CoV-2.
Antiviral Res., 213, 2023
8I5H
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BU of 8i5h by Molmil
Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab Heavy chain, Fab Light chain, ...
Authors:Yamamoto, A, Higashiura, A.
Deposit date:2023-01-25
Release date:2023-04-19
Method:X-RAY DIFFRACTION (2.38 Å)
Cite:Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol, 6, 2023
8I5I
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BU of 8i5i by Molmil
Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab
Descriptor: Fab Heavy chain, Fab Light chain, Spike protein S1
Authors:Yamamoto, A, Higashiura, A.
Deposit date:2023-01-25
Release date:2023-04-19
Method:X-RAY DIFFRACTION (3.06 Å)
Cite:Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol, 6, 2023
7UM2
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BU of 7um2 by Molmil
SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01
Descriptor: Beta-2-microglobulin, CADMIUM ION, HLA class I antigen, ...
Authors:Szeto, C, Gras, S.
Deposit date:2022-04-06
Release date:2023-04-26
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.63 Å)
Cite:SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01
To Be Published
7UR1
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BU of 7ur1 by Molmil
SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01
Descriptor: Beta-2-microglobulin, HLA class I antigen, SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL)
Authors:Szeto, C, Ahn, Y.M, Gras, S.
Deposit date:2022-04-21
Release date:2023-04-26
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.17 Å)
Cite:SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01
To Be Published
7XIK
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BU of 7xik by Molmil
SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex
Descriptor: B38 Fab heavy chain, B38 Fab light chain, Spike protein S1
Authors:Shi, R, Wang, Y, Wu, Z, Han, X, Yan, J.
Deposit date:2022-04-13
Release date:2023-04-26
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.89 Å)
Cite:SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex
To Be Published
7XIL
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BU of 7xil by Molmil
SARS-CoV-2-Beta-RBD and B38-GWP/P-VK antibody complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, B38 Fab heavy chain, B38 Fab light chain, ...
Authors:Shi, R, Wang, Y, Wu, Z, Han, X, Yan, J.
Deposit date:2022-04-13
Release date:2023-04-26
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.91 Å)
Cite:SARS-CoV-2-Beta-RBD and B38-GWP/P-VK antibody complex
To Be Published
7XS8
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BU of 7xs8 by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-1H1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, P5S-1H1 Heavy chain, P5S-1H1 Light chain, ...
Authors:Wang, X, Wang, Z.
Deposit date:2022-05-13
Release date:2023-04-26
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
8DJJ
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BU of 8djj by Molmil
Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Khan, M.B, Lu, J, Young, H.S, Lemieux, M.J.
Deposit date:2022-06-30
Release date:2023-04-26
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.51 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8EIR
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BU of 8eir by Molmil
SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction
Descriptor: 3C-like proteinase nsp5, nsp7-nsp10 of Replicase polyprotein 1a
Authors:Narwal, M, Edwards, T, Armache, J.P, Murakami, K.S.
Deposit date:2022-09-15
Release date:2023-04-26
Last modified:2024-06-19
Method:ELECTRON MICROSCOPY (2.49 Å)
Cite:SARS-CoV-2 polyprotein substrate regulates the stepwise M pro cleavage reaction.
J.Biol.Chem., 299, 2023
8EJ9
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BU of 8ej9 by Molmil
Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-09-16
Release date:2023-04-26
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8GB0
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BU of 8gb0 by Molmil
SARS-CoV-2 Spike H655Y variant, One RBD Open
Descriptor: Spike glycoprotein
Authors:Egri, S.B, Shen, K, Luban, J.
Deposit date:2023-02-24
Release date:2023-04-26
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness.
Biorxiv, 2023
8HEC
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BU of 8hec by Molmil
SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab in the class 2 conformation
Descriptor: 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, ...
Authors:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-11-08
Release date:2023-04-26
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2.
Biochem.Biophys.Res.Commun., 660, 2023
8HED
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BU of 8hed by Molmil
Local refinement of the SARS-CoV-2 Spike trimer in complex with RmAb 9H1 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, Spike protein S1, ...
Authors:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-11-08
Release date:2023-04-26
Method:ELECTRON MICROSCOPY (3.59 Å)
Cite:Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2.
Biochem.Biophys.Res.Commun., 660, 2023

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数据于2024-07-17公开中

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