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 (5197)代表性結構 (2266)最新條目 (44)

7YA1

Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and F375S mutations (local refinement)
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:	Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, G.F.
Deposit date:	2022-06-27
Release date:	2022-08-31
Last modified:	2025-06-25
Method:	ELECTRON MICROSCOPY (3.11 Å)
Cite:	Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat Commun, 13, 2022

7YAD

Cryo-EM structure of S309-RBD-RBD-S309 in the S309-bound Omicron spike protein (local refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, S309 neutralizing antibody heavy chain, S309 neutralizing antibody light chain, ...
Authors:	Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, F.
Deposit date:	2022-06-27
Release date:	2022-08-31
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.66 Å)
Cite:	Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat Commun, 13, 2022

8DDI

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166N Mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Lewandowski, E.M, Jacobs, L.M.C, Chen, Y.
Deposit date:	2022-06-18
Release date:	2022-08-31
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.8 Å)
Cite:	A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations. Plos Pathog., 19, 2023

8DDM

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166R Mutant in Complex with Inhibitor GC376
Descriptor:	(1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5
Authors:	Lewandowski, E.M, Chen, Y.
Deposit date:	2022-06-18
Release date:	2022-08-31
Last modified:	2024-11-06
Method:	X-RAY DIFFRACTION (2.78 Å)
Cite:	A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations. Plos Pathog., 19, 2023

8DLI

Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-10-23
Method:	ELECTRON MICROSCOPY (2.56 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLJ

Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with human 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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-10-30
Method:	ELECTRON MICROSCOPY (2.91 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLL

Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-20
Method:	ELECTRON MICROSCOPY (2.56 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLM

Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with human 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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-06
Method:	ELECTRON MICROSCOPY (2.89 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLO

Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-20
Method:	ELECTRON MICROSCOPY (2.25 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLP

Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human 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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-20
Method:	ELECTRON MICROSCOPY (2.64 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLR

Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8 (focused refinement of NTD and 4-8)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Fab 4-8 heavy chain, Fab 4-8 light chain, ...
Authors:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-06
Method:	ELECTRON MICROSCOPY (2.51 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLS

Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab 4A8 heavy chain, ...
Authors:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.66 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLT

Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.4 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLV

Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein
Authors:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-10-30
Method:	ELECTRON MICROSCOPY (3.11 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLW

Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with Fab S2M11
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab S2M11 heavy chain, ...
Authors:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-10-30
Method:	ELECTRON MICROSCOPY (2.16 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLX

Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with VH ab6
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-13
Method:	ELECTRON MICROSCOPY (2.45 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DLZ

Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:	2022-07-08
Release date:	2022-08-31
Last modified:	2024-11-06
Method:	ELECTRON MICROSCOPY (2.57 Å)
Cite:	SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun, 13, 2022

8DV1

SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion,Immunoglobulin gamma-1 heavy chain, Spike glycoprotein
Authors:	QCRG Structural Biology Consortium, Remesh, S.G, Merz, G.E, Brilot, A.F, Chio, U, Verba, K.A.
Deposit date:	2022-07-27
Release date:	2022-08-31
Last modified:	2024-11-06
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. Structure, 31, 2023

8DV2

SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to computationally engineered ACE2 mimetic CVD293
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion, Spike glycoprotein
Authors:	QCRG Structural Biology Consortium, Remesh, S.G, Merz, G.E, Brilot, A.F, Chio, U, Verba, K.A.
Deposit date:	2022-07-27
Release date:	2022-08-31
Last modified:	2024-10-30
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. Structure, 31, 2023

8DZH

Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with two RBDs down in complex with the Fab fragment of human neutralizing antibody MB.02
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:	Hu, Y, Xiong, Y.
Deposit date:	2022-08-07
Release date:	2022-08-31
Last modified:	2025-05-21
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages. Signal Transduct Target Ther, 8, 2023

7TW9

Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to Sinefungin
Descriptor:	DI(HYDROXYETHYL)ETHER, ETHANOL, METHANOL, ...
Authors:	Kottur, J, Aggarwal, A.K.
Deposit date:	2022-02-06
Release date:	2022-09-07
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.41 Å)
Cite:	High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development. Nat.Struct.Mol.Biol., 29, 2022

8CZI

Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with extended HR2
Descriptor:	Scaffolded Spike protein S2' HR1, Spike protein S2' HR2
Authors:	Yang, K, Brunger, A.T.
Deposit date:	2022-05-24
Release date:	2022-09-07
Last modified:	2024-06-12
Method:	ELECTRON MICROSCOPY (2.22 Å)
Cite:	Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein. Proc.Natl.Acad.Sci.USA, 119, 2022

7F60

Crystal structure of auxiliary protein in complex with human nuclear protein
Descriptor:	Nuclear pore complex protein Nup98-Nup96, ORF6 protein, mRNA export factor
Authors:	Gao, X, Cui, S.
Deposit date:	2021-06-23
Release date:	2022-09-14
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.85 Å)
Cite:	Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport Nat Commun, 13, 2022

7T2U

SARS-CoV2 3C-Like protease complexed with Nemo peptide
Descriptor:	3C-Like Protease, NEMO peptide
Authors:	Wakatsuki, S, Mathews, I.I, Hameedi, M.A.
Deposit date:	2021-12-06
Release date:	2022-09-14
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nat Commun, 13, 2022

7T2V

SARS CoV2 Mpro C145S mutant
Descriptor:	3C-Like Protease
Authors:	Mathews, I.I, Hameedi, M.A, Wakatsuki, S.
Deposit date:	2021-12-06
Release date:	2022-09-14
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (2.47 Å)
Cite:	Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nat Commun, 13, 2022

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