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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
8F0H
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BU of 8f0h by Molmil
Structure of SARS-CoV-2 spike with antibody Fabs 2A10 and 1H2 (Local refinement of the RBD and Fabs 1H2 and 2A10)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody Fab 1H2 heavy chain, Antibody Fab 1H2 light chain, ...
Authors:Yu, X, Zyla, D, Hastie, K.M, Saphire, E.O.
Deposit date:2022-11-02
Release date:2023-05-03
Last modified:2024-11-20
Method:ELECTRON MICROSCOPY (3.18 Å)
Cite:Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.
Cell Rep, 42, 2023
8GS9
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BU of 8gs9 by Molmil
SARS-CoV-2 BA.2 spike RBD in complex bound with VacBB-551
Descriptor: Heavy chain of VacBB-551, Light chain of VacBB-551, Spike glycoprotein
Authors:Liu, C.C, Ju, B, Shen, S.L, Zhang, Z.
Deposit date:2022-09-05
Release date:2023-05-03
Last modified:2024-11-06
Method:ELECTRON MICROSCOPY (2.66 Å)
Cite:Omicron BQ.1.1 and XBB.1 unprecedentedly escape broadly neutralizing antibodies elicited by prototype vaccination.
Cell Rep, 42, 2023
7XSA
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BU of 7xsa by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P2S-2E9 Fab
Descriptor: P2S-2E9 Heavy chain, P2S-2E9 Light chain, Spike protein S1
Authors:Wang, X, Wang, Z.
Deposit date:2022-05-13
Release date:2023-05-10
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
7XSB
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BU of 7xsb by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab
Descriptor: P5S-3B11 Heavy chain, P5S-3B11 Light chain, Spike protein S1
Authors:Wang, X, Wang, Z, Gao, M.
Deposit date:2022-05-13
Release date:2023-05-10
Last modified:2024-10-30
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
8A99
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BU of 8a99 by Molmil
SARS Cov2 Spike in 1-up conformation complex with Fab47
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab47 (Heavy chain variable domain), ...
Authors:Hallberg, B.M, Das, H.
Deposit date:2022-06-28
Release date:2023-05-10
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies.
Immunity, 56, 2023
8H3M
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BU of 8h3m by Molmil
Conformation 1 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy chain, Spike glycoprotein
Authors:Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y.
Deposit date:2022-10-09
Release date:2023-05-10
Last modified:2024-11-13
Method:ELECTRON MICROSCOPY (2.48 Å)
Cite:Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
8H3N
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BU of 8h3n by Molmil
Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy-chain, MO1 light chain, ...
Authors:Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y.
Deposit date:2022-10-09
Release date:2023-05-10
Last modified:2024-10-09
Method:ELECTRON MICROSCOPY (2.73 Å)
Cite:Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
8OT0
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BU of 8ot0 by Molmil
SARS-CoV-2 nsp10-16 methyltransferase in complex with MTA and glycine
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Falke, S.
Deposit date:2023-04-20
Release date:2023-05-10
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (2.21 Å)
Cite:SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery
Elife, 2024
8OV1
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BU of 8ov1 by Molmil
SARS-CoV-2 nsp10-16 methyltransferase in complex with ADP
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D.
Deposit date:2023-04-25
Release date:2023-05-10
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery
Elife, 2024
8BSE
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BU of 8bse by Molmil
CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab
Descriptor: 1D1 FAB HEAVY CHAIN, 1D1 FAB LIGHT CHAIN, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ...
Authors:Welin, M, Kimbung, Y.R, Focht, D, Pisitkun, T.
Deposit date:2022-11-25
Release date:2023-05-17
Last modified:2024-10-09
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants.
Plos One, 18, 2023
8BSF
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BU of 8bsf by Molmil
CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 3D2 FAB HEAVY CHAIN, 3D2 FAB LIGHT CHAIN, ...
Authors:Welin, M, Kimbung, Y.R, Focht, D, Pisitkun, T.
Deposit date:2022-11-25
Release date:2023-05-17
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants.
Plos One, 18, 2023
8CSJ
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BU of 8csj by Molmil
Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein
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-(2-3)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Reddem, E.R, Shapiro, L.
Deposit date:2022-05-12
Release date:2023-05-17
Last modified:2025-06-04
Method:ELECTRON MICROSCOPY (3.53 Å)
Cite:Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein
To Be Published
8FWN
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BU of 8fwn by Molmil
Crystal structure of SARS-CoV-2 papain-like protease C111S mutant
Descriptor: ACETATE ION, CHLORIDE ION, GLYCEROL, ...
Authors:Bezerra, E.H.S, Soprano, A.S, Tonoli, C.C.C, Prado, P.F.V, da Silva, J.C, Franchini, K.G, Trivella, D.B.B, Benedetti, C.E.
Deposit date:2023-01-23
Release date:2023-05-17
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal structure of SARS-CoV-2 papain-like protease C111S mutant
To Be Published
8HN6
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BU of 8hn6 by Molmil
Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD
Descriptor: Heavy chain of monoclonal antibody 3G10, Light chain of monoclonal antibody 3G10, Spike protein S1
Authors:Qi, J, Chen, Y.
Deposit date:2022-12-07
Release date:2023-05-17
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.
Front Immunol, 14, 2023
8HN7
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BU of 8hn7 by Molmil
Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of monoclonal antibody 3C11, Light chain of monoclonal antibody 3C11, ...
Authors:Qi, J, Chen, Y.
Deposit date:2022-12-07
Release date:2023-05-17
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (3 Å)
Cite:Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.
Front Immunol, 14, 2023
8IF2
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BU of 8if2 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor 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, Processed angiotensin-converting enzyme 2, ...
Authors:Kimura, K, Suzuki, T, Hashiguchi, T.
Deposit date:2023-02-17
Release date:2023-05-17
Last modified:2024-11-20
Method:X-RAY DIFFRACTION (2.78 Å)
Cite:Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
Nat Commun, 14, 2023
7XSC
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BU of 7xsc by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-2B10
Descriptor: P5S-2B10 Heavy chain, P5S-2B10 Light chain, Spike protein S1
Authors:Wang, X, Wang, Z, Lin, Z.
Deposit date:2022-05-13
Release date:2023-05-24
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.88 Å)
Cite:Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
8CWI
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BU of 8cwi by Molmil
Fab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Heavy chain of Fab arm of antibody 10G4, ...
Authors:Langley, D.B, Christ, D.
Deposit date:2022-05-19
Release date:2023-05-24
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.873 Å)
Cite:Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies.
Proc.Natl.Acad.Sci.USA, 122, 2025
8CWK
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BU of 8cwk by Molmil
Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Heavy chain of Fab arm of antibody 10G4, ...
Authors:Langley, D.B, Christ, D.
Deposit date:2022-05-19
Release date:2023-05-24
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (2.368 Å)
Cite:Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies.
Proc.Natl.Acad.Sci.USA, 122, 2025
8DNN
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BU of 8dnn by Molmil
Crystal structure of neutralizing antibody 80 in complex with SARS-CoV-2 receptor binding domain
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 80 FAB HEAVY CHAIN, 80 FAB LIGHT CHAIN, ...
Authors:Muthuraman, K, Kucharska, I, Ivanochko, D, Julien, J.P.
Deposit date:2022-07-11
Release date:2023-05-24
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (3.12 Å)
Cite:A multi-specific, multi-affinity antibody platform neutralizes sarbecoviruses and confers protection against SARS-CoV-2 in vivo.
Sci Transl Med, 15, 2023
8GB5
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BU of 8gb5 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9
Descriptor: 25F9 Heavy chain, 25F9 Light chain, BICINE, ...
Authors:Yuan, M, Zhu, X, Wilson, I.A.
Deposit date:2023-02-24
Release date:2023-05-24
Last modified:2024-12-25
Method:X-RAY DIFFRACTION (3.35 Å)
Cite:Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB6
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BU of 8gb6 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 21B6
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, 21B6 Heavy chain, 21B6 Light chain, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2023-02-24
Release date:2023-05-24
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB7
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BU of 8gb7 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 20A7
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 20A7 Heavy chain, 20A7 Light chain, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2023-02-24
Release date:2023-05-24
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.57 Å)
Cite:Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB8
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BU of 8gb8 by Molmil
Crystal structure of SARS-CoV-2 BA.2 receptor binding domain in complex with neutralizing antibody 20A7
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 20A7 Heavy chain, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2023-02-24
Release date:2023-05-24
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8ILC
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BU of 8ilc by Molmil
Crystal structure of Se-Met CoV-Y domain of Nsp3 in SARS-CoV-2
Descriptor: CHLORIDE ION, Papain-like protease nsp3, SULFATE ION
Authors:Wang, K, Nan, J, Lei, J.
Deposit date:2023-03-03
Release date:2023-05-24
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:The CoV-Y domain of SARS-CoV-2 Nsp3 interacts with BRAP to stimulate NF-kappa B signaling and induce host inflammatory responses.
Int.J.Biol.Macromol., 280, 2024

238582

數據於2025-07-09公開中

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