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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
9UHT
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BU of 9uht by Molmil
SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP
Descriptor: Helicase nsp13, Non-structural protein 7, Non-structural protein 8, ...
Authors:Huang, Y.C, Liu, Y.X, Lou, Z.Y, Rao, Z.H, Yan, L.M.
Deposit date:2025-04-14
Release date:2025-06-11
Method:ELECTRON MICROSCOPY (2.89 Å)
Cite:Response to Matter Arising: Substrate selection and transition state support the mechanism for GTP-mediate RNA capping catalyzed by SARS-CoV-2 NiRAN
To Be Published
9C7X
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BU of 9c7x by Molmil
Crystal structure of SARS-CoV-2 antibody 1H06 in complex with a HR2 peptide
Descriptor: Heavy Chain of SARS-CoV-2 antibody 1H06, Light Chain of SARS-CoV-2 antibody 1H06, Spike protein S2'
Authors:Van Wazer, D.J, Zhou, T, Kwong, P.D.
Deposit date:2024-06-11
Release date:2025-06-18
Method:X-RAY DIFFRACTION (1.96 Å)
Cite:SARS-CoV-2 Peptide Immunization in Mice Elicits Broadly Neutralizing Antibodies Targeting Cryptic S2 Helical-Stem Epitope
To Be Published
9EEI
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BU of 9eei by Molmil
Crystal structure of the SARS-CoV-2 Omicron nsp5 main protease (Mpro) E166V mutant in complex with inhibitor GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Neilsen, G, Kirby, K.A, Sarafianos, S.G.
Deposit date:2024-11-19
Release date:2025-06-18
Method:X-RAY DIFFRACTION (2.76 Å)
Cite:Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.
Sci Adv, 11, 2025
9EET
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BU of 9eet by Molmil
Crystal structure of the SARS-CoV-2 nsp5 main protease (Mpro) E166V mutant in complex with inhibitor GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Neilsen, G, Kirby, K.A, Sarafianos, S.G.
Deposit date:2024-11-19
Release date:2025-06-18
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.
Sci Adv, 11, 2025
9EEV
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BU of 9eev by Molmil
Crystal structure of the SARS-CoV-2 Omicron nsp5 main protease (Mpro) E166V mutant in complex with inhibitor Nirmatrelvir (PF-07321332)
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Neilsen, G, Kirby, K.A, Sarafianos, S.G.
Deposit date:2024-11-19
Release date:2025-06-18
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.
Sci Adv, 11, 2025
9FMW
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BU of 9fmw by Molmil
Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6
Descriptor: Fab of neutralizing mAb K501SP6 heavy chain, Fab of neutralizing mAb K501SP6 light chain, Spike glycoprotein,Fibritin
Authors:Bjoernsson, K.H, Walker, M.R, Raghavan, S.S.R, Ward, A.B, Barfod, L.K.
Deposit date:2024-06-07
Release date:2025-06-18
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6
To Be Published
9IKZ
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BU of 9ikz by Molmil
SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3-
Descriptor: BERYLLIUM TRIFLUORIDE ION, GUANOSINE-5'-DIPHOSPHATE, Helicase nsp13, ...
Authors:Yan, L.M, Huang, Y.C, Liu, Y.X, Rao, Z.H, Lou, Z.Y.
Deposit date:2024-06-29
Release date:2025-06-18
Method:ELECTRON MICROSCOPY (3.14 Å)
Cite:Substrate selection and transition reveal the mechanism for RNA capping catalyzed by SARS-CoV-2 NiRAN
To Be Published
9VAO
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BU of 9vao by Molmil
Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2
Descriptor: GLYCEROL, PHOSPHATE ION, Papain-like protease nsp3, ...
Authors:Arya, R, Ganesh, J, Prashar, V, Kumar, M.
Deposit date:2025-06-03
Release date:2025-06-18
Method:X-RAY DIFFRACTION (1.82 Å)
Cite:Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2
To Be Published
9CPP
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BU of 9cpp by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-17 and CC12.3
Descriptor: CC12.3 Fab heavy chain, CC12.3 Fab light chain, CITRIC ACID, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.19 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPQ
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BU of 9cpq by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-44 and CC12.3
Descriptor: CC12.3 Fab heavy chain, CC12.3 Fab light chain, CITRIC ACID, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.88 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPR
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BU of 9cpr by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-90 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPS
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BU of 9cps by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-91 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.03 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPT
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BU of 9cpt by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-92 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.51 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPU
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BU of 9cpu by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0304 and CC12.3
Descriptor: C03-0304 Fab heavy chain, C03-0304 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPV
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BU of 9cpv by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0614 and CC12.3
Descriptor: C03-0614 Fab heavy chain, C03-0614 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPW
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BU of 9cpw by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-1036 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C11-1036 Fab heavy chain, C11-1036 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPX
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BU of 9cpx by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0138 and CC12.3
Descriptor: C03-0138 Fab heavy chain, C03-0138 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPY
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BU of 9cpy by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-0860 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, C11-0860 Fab heavy chain, C11-0860 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9P0F
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BU of 9p0f by Molmil
Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
Descriptor: Non-structural protein 4, SODIUM ION
Authors:Minasov, G, Shuvalova, L, Brunzelle, J.S, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:2025-06-06
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
To Be Published
9CFE
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BU of 9cfe by Molmil
Cryo-EM Local Refinement of Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFF
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BU of 9cff by Molmil
Cryo-EM Refinement of Antibody 19-77 in complex with SARS-CoV-2 HK.3 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFG
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BU of 9cfg by Molmil
Cryo-EM Refinement of Antibody 19-77 R71V in complex with SARS-CoV-2 HK.3 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFH
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BU of 9cfh by Molmil
Cryo-EM Refinement of Antibody 19-77 R71V in complex with SARS-CoV-2 JD.1.1 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9G0H
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BU of 9g0h by Molmil
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17A
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Yang, C.-C, Strater, N, Sylvester, K, Muller, C.E, Yang, M, Lee, M.K, Gao, S, Song, L, Liu, X, Kim, M, Zhan, P.
Deposit date:2024-07-08
Release date:2025-07-02
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Miniaturized Modular Click Chemistry-enabled Rapid Discovery of Unique SARS-CoV-2 M pro Inhibitors With Robust Potency and Drug-like Profile.
Adv Sci, 11, 2024
9G0I
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BU of 9g0i by Molmil
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17B
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, IMIDAZOLE, ...
Authors:Yang, C.-C, Strater, N, Sylvester, K, Muller, C.E, Yang, M, Lee, M.K, Gao, S, Song, L, Liu, X, Kim, M, Zhan, P.
Deposit date:2024-07-08
Release date:2025-07-02
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:Miniaturized Modular Click Chemistry-enabled Rapid Discovery of Unique SARS-CoV-2 M pro Inhibitors With Robust Potency and Drug-like Profile.
Adv Sci, 11, 2024

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數據於2025-07-09公開中

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