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 (5527)代表性結構 (2333)最新條目 (8)

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:	2024-10-16
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:	2024-10-30
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:	2024-10-23
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:	2024-11-20
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:	2024-10-23
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:	2024-10-23
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:	2024-10-23
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:	2024-11-13
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:	2024-11-20
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:	2024-10-23
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:	2024-11-06
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:	2024-10-09
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:	2024-11-13
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:	2024-11-13
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:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.6 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8CYJ

RBD of SARS-CoV-2 Spike protein in complex with pan-sarbecovirus nanobodies 2-10, 2-67, 2-62 and 1-25
Descriptor:	Spike glycoprotein, pan-sarbecovirus nanobody 1-25, pan-sarbecovirus nanobody 2-10, ...
Authors:	Huang, W, Taylor, D.
Deposit date:	2022-05-23
Release date:	2022-07-06
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	Superimmunity by pan-sarbecovirus nanobodies. Cell Rep, 39, 2022

8DCC

SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 3 Bound to P2B-2F6 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, P2B-2F6 Fab heavy chain, P2B-2F6 Fab light chain, ...
Authors:	Dickey, T.D, Tolia, N.H.
Deposit date:	2022-06-16
Release date:	2022-07-06
Last modified:	2024-10-23
Method:	X-RAY DIFFRACTION (2.6 Å)
Cite:	Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response. Sci Adv, 8, 2022

7FB3

SARS-CoV-2 spike protein in one-RBD weak state after CTSL-treatment
Descriptor:	Spike glycoprotein
Authors:	Zhu, Y, Tai, L.H, Sun, F.
Deposit date:	2021-07-08
Release date:	2022-07-13
Last modified:	2025-06-18
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Novel sites for Cathepsin L cleavage in SARS-CoV-2 spike guide treatment strategies To Be Published

7FBJ

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, New antigen receptor variable domain, ...
Authors:	Zhu, J, Xu, T, Feng, B, Liu, J.
Deposit date:	2021-07-11
Release date:	2022-07-13
Last modified:	2024-10-16
Method:	X-RAY DIFFRACTION (2.85 Å)
Cite:	A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape. Small Methods, 6, 2022

7FBK

Crystal structure of SARS-CoV-2 receptor binding domain N501Y mutant in complex with neutralizing nanobody 20G6
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, New antigen receptor variable domain, Spike protein S1
Authors:	Zhu, J, Xu, T, Feng, B, Liu, J.
Deposit date:	2021-07-11
Release date:	2022-07-13
Last modified:	2024-11-06
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape. Small Methods, 6, 2022

7P19

Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2
Descriptor:	1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:	Erausquin, E, Lopez-Sagaseta, J.
Deposit date:	2021-07-01
Release date:	2022-07-13
Last modified:	2024-11-13
Method:	X-RAY DIFFRACTION (3.24 Å)
Cite:	Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution. Acta Crystallogr D Struct Biol, 78, 2022

7WJY

Omicron spike trimer with 6m6 antibody
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 6m6 heavy chain, 6m6 light chain, ...
Authors:	Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
Deposit date:	2022-01-08
Release date:	2022-07-13
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.24 Å)
Cite:	A broadly neutralizing antibody against SARS-CoV-2 Omicron variant infection exhibiting a novel trimer dimer conformation in spike protein binding. Cell Res., 32, 2022

7WK0

Local refine of Omicron spike bitrimer with 6m6 antibody
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 6m6 heavy chain, 6m6 light chain, ...
Authors:	Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
Deposit date:	2022-01-08
Release date:	2022-07-13
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.32 Å)
Cite:	A broadly neutralizing antibody against SARS-CoV-2 Omicron variant infection exhibiting a novel trimer dimer conformation in spike protein binding. Cell Res., 32, 2022

7WON

Cryo-EM structure of SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209 (local refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, VacW-209 heavy chain, ...
Authors:	Zheng, Q, Sun, H, Ju, B, Zhang, Z, Li, S, Xia, N.
Deposit date:	2022-01-22
Release date:	2022-07-13
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.9 Å)
Cite:	Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209. Cell Res., 32, 2022

7WP1

Cryo-EM structure of SARS-CoV-2 Mu S6P trimer in complex with neutralizing antibody VacW-209 (local refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, VacW-209 heavy chain, ...
Authors:	Zheng, Q, Sun, H, Ju, B, Zhang, Z, Li, S, Xia, N.
Deposit date:	2022-01-22
Release date:	2022-07-13
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.77 Å)
Cite:	Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209. Cell Res., 32, 2022

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