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COVID-19特輯

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冠狀病毒
冠狀病毒,2020. 由David S. Goodsell @ RCSB PDB原圖修改

最近爆發的新型冠狀病毒傳染病(Novel Coronavirus disease 2019: COVID-19)對全世界的人們都構成了嚴重威脅。 為了儘早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以開發出有效的抗病毒藥物,已經有很多科研人員開始了相關蛋白結構的研究,並且將所獲得結構數據存儲與PDB。 PDBj為用戶提供了COVID-19相關數據一覽的門戶頁面,並將於每週三更新當日新發佈的相關數據。

有關該病毒蛋白質的解說,請參見下面的“當月的分子”頁面。

“所有結構”標籤的頁面則逐一羅列了所有的數據,包括由同一研究組提交的系列數據群。 “代表性結構”標籤的頁面精選具有相同胺基酸序列的結構數據中的高分辨率數據,不重複選擇具有同一胺基酸序列的數據,即使該數據可能包含不同的配體。 “最新條目”標籤內包含本週新更新數據。


Created: 2020-09-03 (last edited: more than 1 year ago)2022-09-02
6LVN
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BU of 6lvn by Molmil
Structure of the 2019-nCoV HR2 Domain
Descriptor: Spike protein S2'
Authors:Zhu, Y, Sun, F.
Deposit date:2020-02-04
Release date:2020-02-26
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.47 Å)
Cite:Crystal structure of HR2 domain of 2019-nCoV S2 subunit
To Be Published
6LXT
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BU of 6lxt by Molmil
Structure of post fusion core of 2019-nCoV S2 subunit
Descriptor: Spike protein S2, TETRAETHYLENE GLYCOL, ZINC ION
Authors:Zhu, Y, Sun, F.
Deposit date:2020-02-11
Release date:2020-02-26
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion.
Cell Res., 30, 2020
6VW1
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BU of 6vw1 by Molmil
Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Shang, J, Ye, G, Shi, K, Wan, Y.S, Aihara, H, Li, F.
Deposit date:2020-02-18
Release date:2020-03-04
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.68 Å)
Cite:Structural basis of receptor recognition by SARS-CoV-2.
Nature, 581, 2020
6M17
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BU of 6m17 by Molmil
The 2019-nCoV RBD/ACE2-B0AT1 complex
Descriptor: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Yan, R.H, Zhang, Y.Y, Li, Y.N, Xia, L, Guo, Y.Y, Zhou, Q.
Deposit date:2020-02-24
Release date:2020-03-11
Last modified:2024-11-13
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
Science, 367, 2020
6VYB
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BU of 6vyb by Molmil
SARS-CoV-2 spike ectodomain structure (open state)
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:Walls, A.C, Park, Y.J, Tortorici, M.A, Wall, A, Seattle Structural Genomics Center for Infectious Disease (SSGCID), McGuire, A.T, Veesler, D.
Deposit date:2020-02-25
Release date:2020-03-11
Last modified:2024-11-06
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.
Cell, 181, 2020
6VYO
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BU of 6vyo by Molmil
Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, GLYCEROL, ...
Authors:Chang, C, Michalska, K, Jedrzejczak, R, Maltseva, N, Endres, M, Godzik, A, Kim, Y, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-02-27
Release date:2020-03-11
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
Iscience, 27, 2024
6LZG
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BU of 6lzg by Molmil
Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Wang, Q.H, Song, H, Qi, J.X.
Deposit date:2020-02-19
Release date:2020-03-18
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.
Cell, 181, 2020
6M0J
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BU of 6m0j by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, CHLORIDE ION, ...
Authors:Wang, X, Lan, J, Ge, J, Yu, J, Shan, S.
Deposit date:2020-02-21
Release date:2020-03-18
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
Nature, 581, 2020
6W4B
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BU of 6w4b by Molmil
The crystal structure of Nsp9 RNA binding protein of SARS CoV-2
Descriptor: Non-structural protein 9
Authors:Tan, K, Kim, Y, Jedrzejczak, R, Maltseva, N, Endres, M, Michalska, K, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-10
Release date:2020-03-18
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:The crystal structure of Nsp9 replicase protein of COVID-19
To Be Published
6W4H
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BU of 6w4h by Molmil
1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2
Descriptor: 2'-O-methyltransferase, ACETATE ION, Non-structural protein 10, ...
Authors:Minasov, G, Shuvalova, L, Rosas-Lemus, M, Kiryukhina, O, Wiersum, G, Godzik, A, Jaroszewski, L, Stogios, P.J, Skarina, T, Satchell, K.J.F, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-10
Release date:2020-03-18
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.
Sci.Signal., 13, 2020
6W41
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BU of 6w41 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 Fab heavy chain, CR3022 Fab light chain, ...
Authors:Yuan, M, Wu, N.C, Zhu, X.Y, Wilson, I.A.
Deposit date:2020-03-09
Release date:2020-03-25
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (3.084 Å)
Cite:A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV.
Science, 368, 2020
6W61
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BU of 6w61 by Molmil
Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2.
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase, CHLORIDE ION, ...
Authors:Kim, Y, Jedrzejczak, R, Maltseva, N, Endres, M, Godzik, A, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-15
Release date:2020-03-25
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine
Biorxiv, 2020
6YB7
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BU of 6yb7 by Molmil
SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19).
Descriptor: 3C-like proteinase, DI(HYDROXYETHYL)ETHER, DIMETHYL SULFOXIDE
Authors:Owen, C.D, Lukacik, P, Strain-Damerell, C.M, Douangamath, A, Powell, A.J, Fearon, D, Brandao-Neto, J, Crawshaw, A.D, Aragao, D, Williams, M, Flaig, R, Hall, D.R, McAuley, K.E, Mazzorana, M, Stuart, D.I, von Delft, F, Walsh, M.A.
Deposit date:2020-03-16
Release date:2020-03-25
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:COVID-19 main protease with unliganded active site
To Be Published
6M71
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BU of 6m71 by Molmil
SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors
Descriptor: Non-structural protein 7, Non-structural protein 8, RNA-directed RNA polymerase
Authors:Gao, Y, Yan, L, Huang, Y, Liu, F, Cao, L, Wang, T, Wang, Q, Lou, Z, Rao, Z.
Deposit date:2020-03-16
Release date:2020-04-01
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structure of the RNA-dependent RNA polymerase from COVID-19 virus.
Science, 368, 2020
6W9C
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BU of 6w9c by Molmil
The crystal structure of papain-like protease of SARS CoV-2
Descriptor: CHLORIDE ION, Non-structural protein 3, ZINC ION
Authors:Osipiuk, J, Jedrzejczak, R, Tesar, C, Endres, M, Stols, L, Babnigg, G, Kim, Y, Michalska, K, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-22
Release date:2020-04-01
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:The crystal structure of papain-like protease of SARS CoV-2
to be published
6YI3
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BU of 6yi3 by Molmil
The N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein
Descriptor: Nucleoprotein
Authors:Veverka, V, Boura, E.
Deposit date:2020-03-31
Release date:2020-04-08
Last modified:2024-06-19
Method:SOLUTION NMR
Cite:Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein.
Plos Pathog., 16, 2020
6WCF
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BU of 6wcf by Molmil
Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in complex with MES
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Non-structural protein 3
Authors:Michalska, K, Kim, Y, Jedrzejczak, R, Maltseva, N, Endres, M, Mesecar, A, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-30
Release date:2020-04-15
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.065 Å)
Cite:Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes.
Iucrj, 7, 2020
6YLA
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BU of 6yla by Molmil
Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab
Descriptor: 2-(2-METHOXYETHOXY)ETHANOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ...
Authors:Huo, J, Zhao, Y, Ren, J, Zhou, D, Ginn, H.M, Fry, E.E, Owens, R, Stuart, D.I.
Deposit date:2020-04-06
Release date:2020-04-15
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.42 Å)
Cite:Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.
Cell Host Microbe, 28, 2020
7BQY
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BU of 7bqy by Molmil
THE CRYSTAL STRUCTURE OF COVID-19 MAIN PROTEASE IN COMPLEX WITH AN INHIBITOR N3 at 1.7 angstrom
Descriptor: 3C-like proteinase, N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
Authors:Liu, X, Zhang, B, Jin, Z, Yang, H, Rao, Z.
Deposit date:2020-03-26
Release date:2020-04-22
Last modified:2024-10-09
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of Mprofrom SARS-CoV-2 and discovery of its inhibitors.
Nature, 582, 2020
7BV1
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BU of 7bv1 by Molmil
Cryo-EM structure of the apo nsp12-nsp7-nsp8 complex
Descriptor: Non-structural protein 7, Non-structural protein 8, RNA-directed RNA polymerase, ...
Authors:Yin, W, Mao, C, Luan, X, Shen, D, Shen, Q, Su, H, Wang, X, Zhou, F, Zhao, W, Gao, M, Chang, S, Xie, Y.C, Tian, G, Jiang, H.W, Tao, S.C, Shen, J, Jiang, Y, Jiang, H, Xu, Y, Zhang, S, Zhang, Y, Xu, H.E.
Deposit date:2020-04-09
Release date:2020-04-22
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir.
Science, 368, 2020
7BV2
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BU of 7bv2 by Molmil
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Yin, W, Mao, C, Luan, X, Shen, D, Shen, Q, Su, H, Wang, X, Zhou, F, Zhao, W, Gao, M, Chang, S, Xie, Y.C, Tian, G, Jiang, H.W, Tao, S.C, Shen, J, Jiang, Y, Jiang, H, Xu, Y, Zhang, S, Zhang, Y, Xu, H.E.
Deposit date:2020-04-09
Release date:2020-04-22
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir.
Science, 368, 2020
6LZE
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BU of 6lze by Molmil
The crystal structure of COVID-19 main protease in complex with an inhibitor 11a
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zhang, B, Zhang, Y, Jing, Z, Liu, X, Yang, H, Liu, H, Rao, Z, Jiang, H.
Deposit date:2020-02-19
Release date:2020-04-29
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (1.505 Å)
Cite:Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.
Science, 368, 2020
6M0K
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BU of 6m0k by Molmil
The crystal structure of COVID-19 main protease in complex with an inhibitor 11b
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, ~{N}-[(2~{S})-3-(3-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zhang, B, Zhao, Y, Jin, Z, Liu, X, Yang, H, Liu, H, Rao, Z, Jiang, H.
Deposit date:2020-02-22
Release date:2020-04-29
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (1.504 Å)
Cite:Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.
Science, 368, 2020
6W37
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BU of 6w37 by Molmil
STRUCTURE OF THE SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN
Descriptor: ORF7a protein
Authors:Nelson, C.A, Minasov, G, Shuvalova, L, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-09
Release date:2020-04-29
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:STRUCTURE OF THE SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN
To be published
6WEY
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BU of 6wey by Molmil
High-resolution structure of the SARS-CoV-2 NSP3 Macro X domain
Descriptor: Non-structural protein 3
Authors:Vuksanovic, N, Silvaggi, N.R.
Deposit date:2020-04-03
Release date:2020-04-29
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (0.95 Å)
Cite:Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3.
Biochemistry, 59, 2020

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數據於2025-07-02公開中

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