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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
9G9K
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BU of 9g9k by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR2 complex (4.3) bound to AMPNPP
Descriptor: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-01-29
Method:ELECTRON MICROSCOPY (3.34 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
8VUO
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BU of 8vuo by Molmil
Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase, 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE, ...
Authors:Misra, A, Rahisuddin, R, Gupta, Y.K.
Deposit date:2024-01-29
Release date:2025-02-05
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA
To Be Published
8Z6A
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BU of 8z6a by Molmil
Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion 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, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-18
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.99 Å)
Cite:Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation
To Be Published
8Z7B
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BU of 8z7b by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-19
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2)
To Be Published
8Z7G
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BU of 8z7g by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-20
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.06 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)
To Be Published
9CDK
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BU of 9cdk by Molmil
SARS-CoV-2 Mpro A173V mutant in complex with small molecule inhibitor Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Tang, S, Kenneson, J.R, Anderson, K.S.
Deposit date:2024-06-25
Release date:2025-02-05
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.61 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9CDL
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BU of 9cdl by Molmil
SARS-CoV-2 Mpro E166V/L50F double mutant in complex with small molecule inhibitor Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
Authors:Tang, S, Kenneson, J.R, Huynh, K, Anderson, K.S.
Deposit date:2024-06-25
Release date:2025-02-05
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.52 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9G9C
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BU of 9g9c by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR (3.2) complex
Descriptor: CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.72 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9G9D
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BU of 9g9d by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR (4.3) complex
Descriptor: CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
8XSD
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BU of 8xsd by Molmil
BA.5 Spike complex with CR9
Descriptor: CR9 heavy chain, CR9 light chain, Spike glycoprotein
Authors:Feng, L.L.
Deposit date:2024-01-09
Release date:2025-02-12
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.55 Å)
Cite:A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.
Signal Transduct Target Ther, 10, 2025
8Z6S
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BU of 8z6s by Molmil
Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1.
Descriptor: CYFN1006-1 heavy chain, CYFN1006-1 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:Wang, Y.J, Sun, L.
Deposit date:2024-04-19
Release date:2025-02-12
Method:ELECTRON MICROSCOPY (2.84 Å)
Cite:Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1.
To Be Published
8Z6W
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BU of 8z6w by Molmil
Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
Descriptor: CYFN1006-2 heavy chain, CYFN1006-2 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:Wang, Y.J, Sun, L.
Deposit date:2024-04-19
Release date:2025-02-12
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
To Be Published
8Z86
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BU of 8z86 by Molmil
BA.5 RBD in complex with CR9
Descriptor: CR9 heavy chain, CR9 light chain, Spike protein S1
Authors:Feng, L.L.
Deposit date:2024-04-21
Release date:2025-02-12
Last modified:2025-06-18
Method:ELECTRON MICROSCOPY (3.87 Å)
Cite:A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.
Signal Transduct Target Ther, 10, 2025
9BNU
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BU of 9bnu by Molmil
Crystal Structure of T190I SARS-CoV-2 Main Protease
Descriptor: 3C-like proteinase nsp5
Authors:Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BNW
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BU of 9bnw by Molmil
Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease
Descriptor: 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO7
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BU of 9bo7 by Molmil
Crystal Structure of L50F SARS-CoV-2 Main Protease in Complex with Nirmatrelvir
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:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO8
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BU of 9bo8 by Molmil
Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.49 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9EX8
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BU of 9ex8 by Molmil
Free form of a mutant of SARS-CoV-2 main protease Mpro.
Descriptor: Non-structural protein 7
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-05
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EYA
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BU of 9eya by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp4/5 substrate peptide (soaking).
Descriptor: Non-structural protein 7, THR-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-ARG-LYS
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-09
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EZ4
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BU of 9ez4 by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp5/6 substrate peptide.
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLUTAMINE, ...
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-10
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EZ6
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BU of 9ez6 by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp14/15 substrate peptide.
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, DIMETHYL SULFOXIDE, ...
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-10
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9J19
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BU of 9j19 by Molmil
The crystal structure of COVID-19 main protease in complex with an inhibitor minocycline
Descriptor: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE, 3C-like proteinase nsp5
Authors:Singh, A, Jangid, K, Dhaka, P, Tomar, S, Kumar, P.
Deposit date:2024-08-04
Release date:2025-02-12
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural and Mechanistic Insights into the Main Protease (Mpro) Dimer Interface Destabilization Inhibitor: Unveiling New Therapeutic Avenues against SARS-CoV-2.
Biochemistry, 64, 2025
9LAE
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BU of 9lae by Molmil
Locally refined region of SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 3E2, Heavy chain of 9G11, ...
Authors:Jiang, Y, Sun, H, Zheng, Q, Li, S.
Deposit date:2025-01-02
Release date:2025-02-12
Last modified:2025-02-19
Method:ELECTRON MICROSCOPY (3.46 Å)
Cite:Structural insight into broadening SARS-CoV-2 neutralization by an antibody cocktail harbouring both NTD and RBD potent antibodies.
Emerg Microbes Infect, 13, 2024
8VYA
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BU of 8vya by Molmil
SARS-CoV-2 Omicron Variant Spike Glycoprotein Fusion Core (Q954H)
Descriptor: SARS-CoV-2 Omicron variant spike glycoprotein C-terminal heptad repeat domain, SARS-CoV-2 Omicron variant spike glycoprotein N-terminal heptad repeat domain (Q954H)
Authors:Outlaw, V.K, Apurba, R, Vithanage, N.
Deposit date:2024-02-07
Release date:2025-02-19
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:SARS-CoV-2 Omicron Variant Spike Glycoprotein Mutation Q954H Enhances Fusion Core Stability
to be published
8Z4W
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BU of 8z4w by Molmil
Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors
Descriptor: 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone, GLYCEROL, Non-structural protein 3, ...
Authors:Hu, H.C, Xu, Y.C.
Deposit date:2024-04-17
Release date:2025-02-26
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Nonstructural Protein Inhibitors.
J.Am.Chem.Soc., 146, 2024

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數據於2025-07-09公開中

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