COVID-19特輯

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)

所有結構 (4406)代表性結構 (1944)最新條目 (19)

8ZC1

SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region
Descriptor:	Heavy chain of D1F6 Fab, Light chain of D1F6 Fab, Spike protein S1
Authors:	Liu, B, Gao, X, Li, Z, Chen, Q, He, J, Xiong, X.
Deposit date:	2024-04-28
Release date:	2024-05-15
Last modified:	2024-06-12
Method:	ELECTRON MICROSCOPY (4.17 Å)
Cite:	An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep, 43, 2024

8ZC3

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of D1F6 Fab, ...
Authors:	Liu, B, Gao, X, Li, Z, Chen, Q, He, J, Xiong, X.
Deposit date:	2024-04-28
Release date:	2024-05-15
Last modified:	2024-06-12
Method:	ELECTRON MICROSCOPY (4.69 Å)
Cite:	An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep, 43, 2024

8ZC4

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of D1F6 Fab, ...
Authors:	Liu, B, Gao, X, Li, Z, Chen, Q, He, J, Xiong, X.
Deposit date:	2024-04-28
Release date:	2024-05-15
Last modified:	2024-06-12
Method:	ELECTRON MICROSCOPY (3.95 Å)
Cite:	An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep, 43, 2024

8ZC5

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of D1F6 Fab, Light chain of D1F6 Fab, ...
Authors:	Liu, B, Gao, X, Li, Z, Chen, Q, He, J, Xiong, X.
Deposit date:	2024-04-28
Release date:	2024-05-15
Last modified:	2024-06-12
Method:	ELECTRON MICROSCOPY (3.91 Å)
Cite:	An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep, 43, 2024

8C2R

SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CAB-A17 antibody (HC), ...
Authors:	Das, H, Hallberg, B.M.
Deposit date:	2022-12-22
Release date:	2024-05-22
Method:	ELECTRON MICROSCOPY (2.56 Å)
Cite:	SARS-CoV-2 omicron Spike (RBD) in complex with CAB-A17 antibody To Be Published

8JVA

Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N235 and S2L20 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, S2L20 heavy chain, S2L20 light chain, ...
Authors:	Liu, B, Liu, H.H, Han, P, Qi, J.X.
Deposit date:	2023-06-28
Release date:	2024-05-22
Method:	ELECTRON MICROSCOPY (2.81 Å)
Cite:	Enhanced potency of an IgM-like nanobody targeting conserved epitope in SARS-CoV-2 spike N-terminal domain. Signal Transduct Target Ther, 9, 2024

8SWH

Local refinement of SARS-CoV-2 (HP-GSAS-Mut7) spike NTD in complex with TXG-0078 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TXG-0078 Fab Heavy chain, ...
Authors:	Bangaru, B, Ward, A.
Deposit date:	2023-05-18
Release date:	2024-05-22
Last modified:	2024-06-26
Method:	ELECTRON MICROSCOPY (3.88 Å)
Cite:	Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes. Cell Rep, 43, 2024

8JIN

The local refined map of XBB spike protein (S) in complex with bispecific antibody G7-Fc
Descriptor:	7F3 Fv, GW01 Fv, Spike glycoprotein
Authors:	Ma, Y, Mao, Q, Wang, Y, Zhang, Z.
Deposit date:	2023-05-27
Release date:	2024-05-29
Method:	ELECTRON MICROSCOPY (2.45 Å)
Cite:	Structure of XBB spike protein (S) di-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution. To Be Published

8JIO

XBB spike protein (S) in complex with monoclonal antibody 6I18
Descriptor:	6I18 heavy chain, 6I18 light chain, Spike glycoprotein
Authors:	Ma, Y, Mao, Q, Wang, Y, Zhang, Z.
Deposit date:	2023-05-27
Release date:	2024-05-29
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	Structure of XBB spike protein (S) in complex with monoclonal antibody 6I18 at 3.30 Angstroms resolution. To Be Published

8RJZ

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the non-covalent inhibitor GUE-3801 (compound 80 in publication)
Descriptor:	(7~{S})-6-[2-[2,4-bis(chloranyl)phenoxy]ethanoyl]-14-fluoranyl-10-(iminomethyl)-9-methyl-7-(phenylmethyl)-2-oxa-6,9,10-triazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-8-one, 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 3C-like proteinase nsp5, ...
Authors:	Strater, N, Claff, T, Sylvester, K, Mueller, C.E, Guetschow, M, Useini, A.
Deposit date:	2023-12-22
Release date:	2024-05-29
Last modified:	2024-06-19
Method:	X-RAY DIFFRACTION (1.7 Å)
Cite:	Macrocyclic Azapeptide Nitriles: Structure-Based Discovery of Potent SARS-CoV-2 Main Protease Inhibitors as Antiviral Drugs. J.Med.Chem., 67, 2024

8V7T

Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain (residues 1-199)
Descriptor:	Non-structural protein 7
Authors:	Kovalevsky, A, Coates, L.
Deposit date:	2023-12-04
Release date:	2024-05-29
Last modified:	2024-06-12
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease. J.Mol.Biol., 436, 2024

8V7W

Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain C145A precursor, residues nsp4(-6)-1-199-6H
Descriptor:	Replicase polyprotein 1ab
Authors:	Kovalevsky, A, Coates, L.
Deposit date:	2023-12-04
Release date:	2024-05-29
Last modified:	2024-06-12
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease. J.Mol.Biol., 436, 2024

8V8E

Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain (residues 1-199-6H) in complex with ensitrelvir (ESV)
Descriptor:	3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, peptide
Authors:	Kovalevsky, A, Coates, L.
Deposit date:	2023-12-05
Release date:	2024-05-29
Last modified:	2024-06-12
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease. J.Mol.Biol., 436, 2024

8V8G

Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain (residues 1-196) in complex with ensitrelvir (ESV)
Descriptor:	3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:	Kovalevsky, A, Coates, L.
Deposit date:	2023-12-05
Release date:	2024-05-29
Last modified:	2024-06-12
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease. J.Mol.Biol., 436, 2024

8ZC2

SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of D1F6 Fab, ...
Authors:	Liu, B, Gao, X, Li, Z, Chen, Q, He, J, Xiong, X.
Deposit date:	2024-04-28
Release date:	2024-05-29
Last modified:	2024-06-12
Method:	ELECTRON MICROSCOPY (7.82 Å)
Cite:	An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep, 43, 2024

8ZC6

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of D1F6 Fab, Light chain of D1F6 Fab, ...
Authors:	Liu, B, Gao, X, Li, Z, Chen, Q, He, J, Xiong, X.
Deposit date:	2024-04-28
Release date:	2024-05-29
Last modified:	2024-06-12
Method:	ELECTRON MICROSCOPY (6.85 Å)
Cite:	An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep, 43, 2024

8HLC

S protein of SARS-CoV-2 in complex with 3711
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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Zhang, Y.Y, Guo, Y.Y, Zhou, Q.
Deposit date:	2022-11-29
Release date:	2024-06-05
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	A SARS-CoV-2 Spike N-terminal domain neutralizing antibody targets on a glycans shielded silent face and inhibits virus entry via hindering the recognition of RBD and hACE2 To Be Published

8HLD

S protein of SARS-CoV-2 in complex with 26434
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 glycoprotein, ...
Authors:	Zhang, Y.Y, Guo, Y.Y, Zhou, Q.
Deposit date:	2022-11-29
Release date:	2024-06-05
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	A SARS-CoV-2 Spike N-terminal domain neutralizing antibody targets on a glycans shielded silent face and inhibits virus entry via hindering the recognition of RBD and hACE2 To Be Published

8K67

Crystal structure of SARS-CoV-2 3CLpro M165V mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (2.2 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K68

Crystal structure of SARS-CoV-2 3CLpro M49K mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K6A

Crystal structure of SARS-CoV-2 3CLpro S301P mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K6B

Crystal structure of SARS-CoV-2 3CLpro M49K/M165V mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K6C

Crystal structure of SARS-CoV-2 3CLpro M49K/S301P mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (2.21 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K6D

Crystal structure of SARS-CoV-2 3CLpro M49K/S301P mutant in complex with WU-04
Descriptor:	3C-like proteinase nsp5, ~{N}-[(1~{S},2~{R})-2-[[4-bromanyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]isoquinoline-4-carboxamide
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (1.65 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8P5M

SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab)
Descriptor:	Mab-23 (Heavy chain variable domain), Mab-23 (Light chain variable domain), Spike protein S1
Authors:	Das, H, Hallberg, B.M.
Deposit date:	2023-05-24
Release date:	2024-06-05
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab domains) To Be Published

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