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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
8XEF
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BU of 8xef by Molmil
Cocktail GC2050-GC2225
Descriptor: GC2050 heavy chain, GC2050 light chain, GC2225 heavy chain, ...
Authors:Feng, L.L.
Deposit date:2023-12-11
Release date:2024-12-11
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (4.41 Å)
Cite:XBB.1.5 RBD in complex with GC2050 and GC2225
To Be Published
9CJ6
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BU of 9cj6 by Molmil
Crystal Structure of SARS-CoV-2 N-NTD with part of N-arm complex with ssDNA.
Descriptor: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), Nucleoprotein
Authors:Maiti, A, Matsuo, H.
Deposit date:2024-07-05
Release date:2024-12-11
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Affinity Tag-Free Purification of SARS-CoV-2 N Protein and Its Crystal Structure in Complex with ssDNA.
Biomolecules, 14, 2024
8JAP
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BU of 8jap by Molmil
Cryo-EM structure of SARS-CoV-2 WT RBD in complex with W328-6H2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, H chain of W328-6H2 Fab region, L chain of W328-6H2 Fab region, ...
Authors:Nan, X.Y, Li, Y.J.
Deposit date:2023-05-06
Release date:2024-12-18
Method:ELECTRON MICROSCOPY (3.81 Å)
Cite:Cryo-EM structure of SARS-CoV-2 WT RBD in complex with W328-6H2 (local refinement)
To Be Published
8V5V
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BU of 8v5v by Molmil
Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open 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, Spike protein S2,Fibritin, ...
Authors:Olmedillas, E, Diaz, R, Hastie, K, Ollmann-Saphire, E.
Deposit date:2023-12-01
Release date:2024-12-18
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
To Be Published
8XRQ
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BU of 8xrq by Molmil
SARS-CoV-2 BA.1 spike RBD in complex bound with VacBB-639
Descriptor: Heavy chain of VacBB 639 Fab, Light chain of VacBB 639 Fab, Spike protein S1
Authors:Liu, C.C, Ju, B, Zhang, Z.
Deposit date:2024-01-08
Release date:2024-12-18
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (4.19 Å)
Cite:Rapid clonal expansion and somatic hypermutation contribute to the fate of SARS-CoV-2 broadly neutralizing antibodies.
J Immunol., 214, 2025
9BIH
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BU of 9bih by Molmil
SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA with 1 nucleotide bulge
Descriptor: RNA (34-mer), RNA (35-mer), Uridylate-specific endoribonuclease nsp15
Authors:Wright, Z.M, Butay, K.J, Krahn, J.M, Borgnia, M.J, Stanley, R.E.
Deposit date:2024-04-23
Release date:2024-12-18
Last modified:2025-01-15
Method:ELECTRON MICROSCOPY (3.24 Å)
Cite:Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates.
Nat Commun, 16, 2025
8ZPP
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BU of 8zpp by Molmil
Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab
Descriptor: Spike glycoprotein,Fibritin, variable heavy chain of ORB10 Fab, variable light chain of ORB10 Fab
Authors:Cao, S, Leng, C, Hu, H.
Deposit date:2024-05-30
Release date:2024-12-25
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab
To Be Published
9BF9
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BU of 9bf9 by Molmil
Human LAG-3-HLA-DR1 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, DI(HYDROXYETHYL)ETHER, HLA class II histocompatibility antigen DR beta chain, ...
Authors:Petersen, J, Rossjohn, J.
Deposit date:2024-04-17
Release date:2024-12-25
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:Crystal structure of the human LAG-3-HLA-DR1-peptide complex.
Sci Immunol, 9, 2024
8RJ5
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BU of 8rj5 by Molmil
P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex
Descriptor: Beta-2-microglobulin, MHC class I antigen, P1-15 T-cell Receptor Alpha Chain, ...
Authors:Wall, A, Sewell, A.K, Motozono, C, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-20
Release date:2025-01-01
Method:X-RAY DIFFRACTION (3.02 Å)
Cite:NF9 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex (Paper Pending)
To Be Published
8RJH
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BU of 8rjh by Molmil
HLA A*2402-NF9_6F pMHC complex
Descriptor: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE, Beta-2-microglobulin, MHC class I antigen
Authors:Wall, A, Sewell, A.K, Motozono, C, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-21
Release date:2025-01-01
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:HLA A*2402-NF9_6F pMHC complex
To Be Published
8RJI
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BU of 8rji by Molmil
HLA A*2402-NF9_5R pMHC complex
Descriptor: Beta-2-microglobulin, MHC class I antigen, Spike glycoprotein
Authors:Wall, A, Motozono, C, Sewell, A.K, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-21
Release date:2025-01-01
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:HLA A*2402-NF9_5R pMHC complex
To Be Published
8Y4D
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BU of 8y4d by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{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:Zhou, X.L, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-01-30
Release date:2025-01-08
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Crystal structure of SARS-Cov-2 main protease in complex with Bofutrelvir
To Be Published
8Y4G
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BU of 8y4g by Molmil
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{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:Zeng, P, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-01-30
Release date:2025-01-08
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
8Y4H
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BU of 8y4h by Molmil
Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{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:Guo, L, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-01-30
Release date:2025-01-08
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
8YDP
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BU of 8ydp by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SARS-CoV-2 inhibiting peptide Ce9, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDQ
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BU of 8ydq by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with Ce149
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide Ce149, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDR
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BU of 8ydr by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce59
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 inhibiting peptide Ce59, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDS
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BU of 8yds by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike protein in complex with Ce59
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SARS-CoV-2 inhibiting peptide Ce59, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDT
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BU of 8ydt by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce41
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 inhibiting peptide Ce41, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDU
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BU of 8ydu by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDV
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BU of 8ydv by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDW
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BU of 8ydw by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, SODIUM ION, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDX
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BU of 8ydx by Molmil
Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.2 variant) in complex with CeSPIACE
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CeSPIACE, Spike glycoprotein
Authors:Suzuki, H, Nakamura, S, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:ELECTRON MICROSCOPY (4.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDZ
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BU of 8ydz by Molmil
Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CeSPIACE, Spike glycoprotein
Authors:Suzuki, H, Nakamura, S, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:ELECTRON MICROSCOPY (5.2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
9IUP
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BU of 9iup by Molmil
KP.3 RBD in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Feng, L.L.
Deposit date:2024-07-22
Release date:2025-01-15
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2.
Cell Discov, 10, 2024

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數據於2025-07-09公開中

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