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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
9B0Y
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BU of 9b0y by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-03-12
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.32 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9BJ2
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BU of 9bj2 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1533 (local refinement of NTD and C1533)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, C1533 Heavy Chain, C1533 Light Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9BJ3
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BU of 9bj3 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1596
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C1596 Fab Heavy Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9BJ4
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BU of 9bj4 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C952
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C952 Heavy Chain, C952 Light Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9CXE
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BU of 9cxe by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation -C1
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-07-31
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.48 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9I81
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BU of 9i81 by Molmil
SARS-CoV-2 RdRp bound to a stack of three HeE1-2Tyr molecules
Descriptor: N-[8-(cyclohexyloxy)-1-oxo-2-phenyl-1H-pyrido[2,1-b][1,3]benzothiazole-4-carbonyl]-L-tyrosine, Non-structural protein 7, Non-structural protein 8, ...
Authors:Kabinger, F, Doze, V, Schmitzova, J, Lidschreiber, M, Dienemann, C, Cramer, P.
Deposit date:2025-02-04
Release date:2025-03-05
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (2.98 Å)
Cite:Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr.
Proc.Natl.Acad.Sci.USA, 122, 2025
8YK4
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BU of 8yk4 by Molmil
Structure of SARS-CoV-2 RBD and antibody NT-108
Descriptor: Spike protein S1, antibody NT-108, single chain Fv fragment
Authors:Anraku, Y, Kita, S, Onodera, T, Sato, A, Tadokoro, T, Adachi, Y, Ito, S, Suzuki, T, Sasaki, J, Shiwa, N, Iwata, N, Nagata, N, Kazuki, Y, Oshimura, M, Sasaki, M, Orba, Y, Suzuki, T, Sawa, H, Hashiguchi, T, Fukuhara, H, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-04
Release date:2025-03-12
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structural Basis for Potent Neutralization Activity of SARS-CoV-2 Antibody, NT-108
To Be Published
8YKG
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BU of 8ykg by Molmil
Structure of SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (1-up 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, NT-108 scFv, ...
Authors:Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-05
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.28 Å)
Cite:Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
8YKH
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BU of 8ykh by Molmil
Structure of SARS-CoV-2 spike RBD in complex with NT-108 scFv
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NT-108 scFv, Spike glycoprotein
Authors:Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-05
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.27 Å)
Cite:Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
9BLL
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BU of 9bll by Molmil
Cryo-EM of RBD(EG5.1)/1301B7 Fab Complex
Descriptor: 1301B7 Heavy Chain, 1301B7 Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Walter, M.R, Green, T.J.
Deposit date:2024-04-30
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:Potent neutralization by a RBD antibody with broad specificity for SARS-CoV-2 JN.1 and other variants.
Npj Viruses, 2, 2024
9CCI
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BU of 9cci by Molmil
Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, M39 Fab heavy chain, M39 Fab light chain, ...
Authors:Bajic, G, Jaiswal, D.
Deposit date:2024-06-21
Release date:2025-03-12
Last modified:2025-05-28
Method:ELECTRON MICROSCOPY (2.65 Å)
Cite:Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.
Biorxiv, 2024
9CCJ
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BU of 9ccj by Molmil
Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, M2 Fab Heavy Chain, ...
Authors:Bajic, G, Civljak, A.
Deposit date:2024-06-21
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (2.37 Å)
Cite:Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.
Biorxiv, 2024
9CGV
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BU of 9cgv by Molmil
SARS-CoV-2 nsp12 NiRAN domain bound to a covalent inhibitor SW090466-1
Descriptor: MANGANESE (II) ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Osinski, A, Hernandez, G, Tagliabracci, V.S.
Deposit date:2024-07-01
Release date:2025-03-12
Last modified:2025-04-23
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine.
J.Biol.Chem., 301, 2025
9J66
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BU of 9j66 by Molmil
Cryo-EM structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment CAV-C65 (local refinement)
Descriptor: CAV-C65 Heavy chain, CAV-C65 Light chain, Spike protein S1
Authors:Jing, X, Chen, Y, Gong, P.
Deposit date:2024-08-15
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.55 Å)
Cite:IgA class switching enhances neutralizing potency against SARS-CoV-2 by increased antibody hinge flexibility.
Antiviral Res., 235, 2025
9N55
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BU of 9n55 by Molmil
X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
Descriptor: N-OCTANE, ORF9b protein
Authors:San Felipe, C.J, Fraser, J.S.
Deposit date:2025-02-03
Release date:2025-03-12
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
To Be Published
8UTC
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BU of 8utc by Molmil
HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
Descriptor: Beta-2-microglobulin, CHLORIDE ION, HLA class I histocompatibility antigen, ...
Authors:Oltean, N, Nyovanie, S, Hashem, A, Patskovska, L, Patskovsky, Y, Krogsgaard, M.
Deposit date:2023-10-30
Release date:2025-03-19
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
To Be Published
8Z1H
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BU of 8z1h by Molmil
Crystal structure of SARS main protease in complex with PF-00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Lin, C, Zhang, J, Li, J.
Deposit date:2024-04-11
Release date:2025-03-19
Method:X-RAY DIFFRACTION (2.61 Å)
Cite:Crystal structure of SARS main protease in complex with PF-00835231
To Be Published
9DJ8
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BU of 9dj8 by Molmil
RNA-nsp9 bound to the NiRAN domain of the E-RTC with an empty G-pocket
Descriptor: ADENOSINE MONOPHOSPHATE, Non-structural protein 9, RNA-directed RNA polymerase, ...
Authors:Small, G.I, Darst, S.A, Campbell, E.A.
Deposit date:2024-09-06
Release date:2025-03-19
Method:ELECTRON MICROSCOPY (2.58 Å)
Cite:Matters arising: There is no structure of the catalytic intermediate of GTP-mediated mRNA capping by the SARS-CoV-2 NiRAN domain, and thus the mechanism remains unknown
To Be Published
9L09
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BU of 9l09 by Molmil
SARS-CoV-2 C-RTC with 13-TP
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Huang, Y.C, Liang, L, Liu, Y.X, Yan, L.M, Lou, Z.Y, Rao, Z.H.
Deposit date:2024-12-12
Release date:2025-03-19
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Discovery of a 2'-a-Fluoro-2'-b-C-(fluoromethyl) Purine Nucleotide Prodrug as a Potential Oral Anti-SARS-CoV-2 Agent
J Med Chem, 68, 2025
9L6C
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BU of 9l6c by Molmil
Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Fab ConD-852, Heavy chain of Fab P2C-1F11, ...
Authors:Zheng, Z, Bing, J, Congcong, L, Bing, Z.
Deposit date:2024-12-24
Release date:2025-03-19
Method:ELECTRON MICROSCOPY (3.33 Å)
Cite:Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs
To Be Published
8ZYF
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BU of 8zyf by Molmil
Crystal structure of ZW2G10 Fab in complex with omicron RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, ZW2G10 fab heavy chain, ...
Authors:Yuan, H.Y, Li, J.M.
Deposit date:2024-06-17
Release date:2025-03-26
Last modified:2025-04-16
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Nasal delivery of secretory IgA confers enhanced neutralizing activity against Omicron variants compared to its IgG counterpart.
Mol.Ther., 33, 2025
9GXE
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BU of 9gxe by Molmil
Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
Descriptor: 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A.
Deposit date:2024-09-30
Release date:2025-03-26
Method:ELECTRON MICROSCOPY (2.3 Å)
Cite:Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
To Be Published
9GXG
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BU of 9gxg by Molmil
Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
Descriptor: 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone, 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A.
Deposit date:2024-09-30
Release date:2025-03-26
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (1.92 Å)
Cite:Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
To Be Published
8YWE
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BU of 8ywe by Molmil
Local refinement of SARS-CoV-2 Omicron BA.2.86 S complexed with Abs G7-Fc
Descriptor: 7F3 scFv, GW01 scFv, Spike protein S1
Authors:Ma, Y, Liu, Q, Rehati, P, Zhang, Z.
Deposit date:2024-03-31
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (2.69 Å)
Cite:Impact of scFv Sequence and Position on the Functionality of Bispecific Antibodies against Omicron Variants EG.5 and BA.2.86
To Be Published
8ZFV
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BU of 8zfv by Molmil
Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone
Descriptor: Ceftriaxone, DI(HYDROXYETHYL)ETHER, Nucleoprotein, ...
Authors:Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
Deposit date:2024-05-08
Release date:2025-04-02
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
J.Struct.Biol., 217, 2025

238582

數據於2025-07-09公開中

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