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)

5SSP

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5459166285 - (R,R) and (S,S) isomers
Descriptor:	(1R,2R)-4-hydroxy-1-[(1H-indole-5-carbonyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid, (1S,2S)-4-hydroxy-1-[(1H-indole-5-carbonyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid, Non-structural protein 3
Authors:	Correy, G.J, Fraser, J.S.
Deposit date:	2022-06-09
Release date:	2022-07-06
Last modified:	2023-09-20
Method:	X-RAY DIFFRACTION (1.15 Å)
Cite:	Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 120, 2023

5SSQ

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5459166291
Descriptor:	3-{[(1H-benzimidazole-5-carbonyl)amino]methyl}-1H-indole-2-carboxylic acid, Non-structural protein 3
Authors:	Correy, G.J, Fraser, J.S.
Deposit date:	2022-06-09
Release date:	2022-07-06
Last modified:	2023-09-20
Method:	X-RAY DIFFRACTION (1.15 Å)
Cite:	Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 120, 2023

5SSR

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5459166300
Descriptor:	3-{[(2-hydroxy-1H-benzimidazole-5-carbonyl)amino]methyl}-1H-indole-2-carboxylic acid, Non-structural protein 3
Authors:	Correy, G.J, Fraser, J.S.
Deposit date:	2022-06-09
Release date:	2022-07-06
Last modified:	2023-09-20
Method:	X-RAY DIFFRACTION (1.15 Å)
Cite:	Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 120, 2023

7TUQ

Crystal structure of BRD4 bromodomain 1 in complex with monoacetylated SARS-CoV-2 E
Descriptor:	Bromodomain-containing protein 4, Envelope small membrane protein
Authors:	Vann, K.R, Kutateladze, T.G.
Deposit date:	2022-02-03
Release date:	2022-07-06
Last modified:	2023-11-15
Method:	X-RAY DIFFRACTION (2.68 Å)
Cite:	Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection. Structure, 30, 2022

7TV0

Crystal structure of BRD4 bromodomain 1 in complex with dual-acetylated SARS-CoV-2 E
Descriptor:	Bromodomain-containing protein 4, Envelope small membrane protein
Authors:	Vann, K.R, Holt, T.A, Kutateladze, T.G.
Deposit date:	2022-02-03
Release date:	2022-07-06
Last modified:	2023-11-15
Method:	X-RAY DIFFRACTION (2.6 Å)
Cite:	Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection. Structure, 30, 2022

7VBE

1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0
Descriptor:	Nucleoprotein
Authors:	Zhou, X.L, Zhong, F.L, Li, J, Zhang, J.
Deposit date:	2021-08-31
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.59 Å)
Cite:	1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0 To Be Published

7VBF

1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5
Descriptor:	Nucleoprotein
Authors:	Zhou, X.L, Zhong, F.L, Li, J, Zhang, J.
Deposit date:	2021-08-31
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.3 Å)
Cite:	1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5 To Be Published

7X1M

The complex structure of Omicron BA.1 RBD with BD604, S309,and S304
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, BD-604 Fab heavy chain, BD-604 Fab light chain, ...
Authors:	Huang, M, Xie, Y.F, Qi, J.X.
Deposit date:	2022-02-24
Release date:	2022-07-06
Last modified:	2023-07-19
Method:	ELECTRON MICROSCOPY (2.74 Å)
Cite:	Atlas of currently available human neutralizing antibodies against SARS-CoV-2 and escape by Omicron sub-variants BA.1/BA.1.1/BA.2/BA.3. Immunity, 55, 2022

7X6J

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3af
Descriptor:	3C-like proteinase, quinoline-2-carboxylic acid
Authors:	Su, H, Nie, T, Xie, H, Li, Z.W, Li, M.J, Xu, Y.
Deposit date:	2022-03-07
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination. J.Med.Chem., 65, 2022

7X6K

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3w
Descriptor:	1H-indole-2-carbaldehyde, 3C-like proteinase
Authors:	Su, H, Nie, T, Xie, H, Li, Z.W, Li, M.J, Xu, Y.
Deposit date:	2022-03-07
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.34 Å)
Cite:	Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination. J.Med.Chem., 65, 2022

7XAZ

Crystal structure of Omicron BA.1.1 RBD complexed with hACE2
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:	Liao, H, Meng, Y, Li, W.
Deposit date:	2022-03-19
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell, 185, 2022

7XB0

Crystal structure of Omicron BA.2 RBD complexed with hACE2
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:	Li, L, Liao, H, Meng, Y, Li, W.
Deposit date:	2022-03-19
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.9 Å)
Cite:	Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell, 185, 2022

7XB1

Crystal structure of Omicron BA.3 RBD complexed with hACE2
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:	Li, W, Meng, Y, Liao, H.
Deposit date:	2022-03-19
Release date:	2022-07-06
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.7 Å)
Cite:	Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell, 185, 2022

7Y42

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein in complex with all-trans retinoic acid
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, RETINOIC ACID, Spike glycoprotein
Authors:	Xiang, Y, Wang, L.
Deposit date:	2022-06-13
Release date:	2022-07-06
Last modified:	2022-09-14
Method:	ELECTRON MICROSCOPY (3.45 Å)
Cite:	A Retinol Derivative Inhibits SARS-CoV-2 Infection by Interrupting Spike-Mediated Cellular Entry. Mbio, 13, 2022

8CWU

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 1-21
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, VHH 1-21
Authors:	Liu, H, Wilson, I.A.
Deposit date:	2022-05-19
Release date:	2022-07-06
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.71 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CWV

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.1 Fab heavy chain, CC12.1 Fab light chain, ...
Authors:	Liu, H, Wilson, I.A.
Deposit date:	2022-05-19
Release date:	2022-07-06
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.51 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CXN

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-57
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, pan-sarbecovirus nanobody 2-57
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-22
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CXQ

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-22
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 1-22
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-22
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.3 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CY6

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-65
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 2-65
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CY7

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34
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:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CY9

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-23
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 1-23
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYA

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-67
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:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.7 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYB

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-8
Descriptor:	1-deoxy-alpha-D-mannopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.7 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYC

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 2-34
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYD

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-45
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 2-45
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.6 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

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