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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
7KRS
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BU of 7krs by Molmil
Structural impact on SARS-CoV-2 spike protein by D614G substitution
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:Zhang, J, Cai, Y.F, Xiao, T.S, Lu, J.M, Peng, H.Q, Sterling, S.M, Walsh Jr, R.M, Volloch, S.R, Zhu, H.S, Woosley, A.N, Yang, W, Sliz, P, Chen, B.
Deposit date:2020-11-20
Release date:2021-03-24
Last modified:2021-05-12
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Structural impact on SARS-CoV-2 spike protein by D614G substitution.
Science, 372, 2021
7L2D
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BU of 7l2d by Molmil
Cryo-EM structure of NTD-directed neutralizing antibody 1-87 in complex with prefusion SARS-CoV-2 spike glycoprotein
Descriptor: 1-87 heavy chain, 1-87 light chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Cerutti, G, Shapiro, L.
Deposit date:2020-12-16
Release date:2021-03-24
Last modified:2021-05-26
Method:ELECTRON MICROSCOPY (3.55 Å)
Cite:Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.
Cell Host Microbe, 29, 2021
7L2E
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BU of 7l2e by Molmil
Cryo-EM structure of NTD-directed neutralizing antibody 4-18 in complex with prefusion SARS-CoV-2 spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 4-18 heavy chain, ...
Authors:Cerutti, G, Shapiro, L.
Deposit date:2020-12-16
Release date:2021-03-24
Last modified:2021-05-26
Method:ELECTRON MICROSCOPY (2.97 Å)
Cite:Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.
Cell Host Microbe, 29, 2021
7L2F
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BU of 7l2f by Molmil
Cryo-EM structure of NTD-directed neutralizing antibody 5-24 in complex with prefusion SARS-CoV-2 spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 5-24 heavy chain, ...
Authors:Cerutti, G, Shapiro, L.
Deposit date:2020-12-16
Release date:2021-03-24
Last modified:2021-05-26
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.
Cell Host Microbe, 29, 2021
7LQV
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BU of 7lqv by Molmil
Cryo-EM structure of NTD-directed neutralizing antibody 4-8 Fab in complex with SARS-CoV-2 S2P spike
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-8 Heavy Chain, 4-8 Light chain, ...
Authors:Gorman, J, Rapp, M, Kwong, P.D, Shapiro, L.
Deposit date:2021-02-15
Release date:2021-03-24
Method:ELECTRON MICROSCOPY (3.25 Å)
Cite:Potent SARS-CoV-2 Neutralizing Antibodies Directed Against Spike N-Terminal Domain Target a Single Supersite
Cell Host Microbe, 2021
7LQW
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BU of 7lqw by Molmil
Cryo-EM structure of NTD-directed neutralizing antibody 2-17 Fab in complex with SARS-CoV-2 S2P spike
Descriptor: 2-17 Heavy Chain, 2-17 Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Gorman, J, Rapp, M, Kwong, P.D, Shapiro, L.
Deposit date:2021-02-15
Release date:2021-03-24
Last modified:2021-05-26
Method:ELECTRON MICROSCOPY (4.47 Å)
Cite:Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.
Cell Host Microbe, 29, 2021
7DEO
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BU of 7deo by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Spike protein S1, ...
Authors:Fu, D, Zhang, G, Li, X, Rao, Z, Guo, Y.
Deposit date:2020-11-04
Release date:2021-03-31
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes.
Plos Biol., 19, 2021
7DET
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BU of 7det by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, antibody scFv
Authors:Wang, Y, Zhang, G, Li, X, Rao, Z, Guo, Y.
Deposit date:2020-11-05
Release date:2021-03-31
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes.
Plos Biol., 19, 2021
7DEU
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BU of 7deu by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, antibody scFv
Authors:Zhang, Z, Zhang, G, Li, X, Rao, Z, Guo, Y.
Deposit date:2020-11-05
Release date:2021-03-31
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes.
Plos Biol., 19, 2021
7DWX
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BU of 7dwx by Molmil
Conformation 1 of S-ACE2-B0AT1 ternary complex
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:Yan, R.H, Zhang, Y.Y, Li, Y.N, Ye, F.F, Guo, Y.Y, Xia, L, Zhong, X.Y, Chi, X.M, Zhou, Q.
Deposit date:2021-01-18
Release date:2021-03-31
Last modified:2021-06-16
Method:ELECTRON MICROSCOPY (8.3 Å)
Cite:Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2.
Cell Res., 31, 2021
7DWY
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BU of 7dwy by Molmil
S protein of SARS-CoV-2 in the locked 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, LINOLEIC ACID, ...
Authors:Yan, R.H, Zhang, Y.Y, Li, Y.N, Ye, F.F, Guo, Y.Y, Xia, L, Zhong, X.Y, Chi, X.M, Zhou, Q.
Deposit date:2021-01-18
Release date:2021-03-31
Last modified:2021-06-16
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2.
Cell Res., 31, 2021
7DX1
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BU of 7dx1 by Molmil
S protein of SARS-CoV-2 D614G mutant
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:Yan, R.H, Zhang, Y.Y, Li, Y.N, Ye, F.F, Guo, Y.Y, Xia, L, Zhong, X.Y, Chi, X.M, Zhou, Q.
Deposit date:2021-01-18
Release date:2021-03-31
Last modified:2021-06-16
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2.
Cell Res., 31, 2021
7DX8
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BU of 7dx8 by Molmil
Trypsin-digested S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 2 (2 up RBD and 2 PD bound)
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:Yan, R.H, Zhang, Y.Y, Li, Y.N, Ye, F.F, Guo, Y.Y, Xia, L, Zhong, X.Y, Chi, X.M, Zhou, Q.
Deposit date:2021-01-18
Release date:2021-03-31
Last modified:2021-06-16
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2.
Cell Res., 31, 2021
7EAN
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BU of 7ean by Molmil
immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 6D6
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of SARS-CoV-2 cross-neutralizing mAb 6D6, Light chain of SARS-CoV-2 cross-neutralizing mAb 6D6, ...
Authors:Li, T.T, Gu, Y, Li, S.W.
Deposit date:2021-03-07
Release date:2021-03-31
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Cross-neutralizing antibodies bind a SARS-CoV-2 cryptic site and resist circulating variants.
Nat Commun, 12, 2021
7LJR
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BU of 7ljr by Molmil
SARS-CoV-2 Spike Protein Trimer bound to DH1043 fab
Descriptor: Fab DH1043 heavy chain, Fab DH1043 light chain, Spike glycoprotein
Authors:Gobeil, S, Acharya, P.
Deposit date:2021-01-30
Release date:2021-03-31
Last modified:2024-03-06
Method:ELECTRON MICROSCOPY (3.66 Å)
Cite:The functions of SARS-CoV-2 neutralizing and infection-enhancing antibodies in vitro and in mice and nonhuman primates.
Biorxiv, 2021
7LM8
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BU of 7lm8 by Molmil
Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with two cross-neutralizing antibodies CV38-142 and COVA1-16 Fabs isolated from COVID-19 patients
Descriptor: 1,2-ETHANEDIOL, COVA1-16 Fab heavy chain, COVA1-16 Fab light chain, ...
Authors:Liu, H, Wilson, I.A.
Deposit date:2021-02-05
Release date:2021-03-31
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.936 Å)
Cite:A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection.
Cell Host Microbe, 29, 2021
7LO4
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BU of 7lo4 by Molmil
SARS-CoV-2 spike receptor-binding domain with a G485R mutation in complex with human ACE2
Descriptor: 1,2-ETHANEDIOL, 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:Weekley, C.M, Parker, M.W.
Deposit date:2021-02-09
Release date:2021-03-31
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.465 Å)
Cite:SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2
Biorxiv, 2021
7LWM
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BU of 7lwm by Molmil
Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up 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 glycoprotein
Authors:Gobeil, S, Acharya, P.
Deposit date:2021-03-01
Release date:2021-03-31
Last modified:2021-08-18
Method:ELECTRON MICROSCOPY (2.83 Å)
Cite:Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
Science, 373, 2021
7LWV
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BU of 7lwv by Molmil
UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Gobeil, S, Acharya, P.
Deposit date:2021-03-01
Release date:2021-03-31
Last modified:2021-08-18
Method:ELECTRON MICROSCOPY (3.12 Å)
Cite:Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
Science, 373, 2021
7LWW
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BU of 7lww by Molmil
Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 1-RBD-up conformation (S-GSAS-D614G-K417N-E484K-N501Y)
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:Gobeil, S, Acharya, P.
Deposit date:2021-03-01
Release date:2021-03-31
Last modified:2021-08-18
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
Science, 373, 2021
7LYO
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BU of 7lyo by Molmil
South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Gobeil, S, Acharya, P.
Deposit date:2021-03-07
Release date:2021-03-31
Last modified:2022-12-07
Method:ELECTRON MICROSCOPY (3.32 Å)
Cite:Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
Science, 373, 2021
7M4R
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BU of 7m4r by Molmil
Structural basis for SARS-CoV-2 envelope protein in recognition of human cell junction protein PALS1
Descriptor: Envelope small membrane protein, MAGUK p55 subfamily member 5
Authors:Liu, Q, Chai, J.
Deposit date:2021-03-22
Release date:2021-03-31
Last modified:2024-03-06
Method:ELECTRON MICROSCOPY (3.65 Å)
Cite:Structural basis for SARS-CoV-2 envelope protein recognition of human cell junction protein PALS1.
Nat Commun, 12, 2021
7D4G
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BU of 7d4g by Molmil
A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2
Descriptor: Heavy chain of FC05 Fab, Light chain of FC05 Fab, Spike glycoprotein S1
Authors:Cao, L, Wang, X.
Deposit date:2020-09-23
Release date:2021-04-07
Last modified:2022-02-23
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2.
Natl Sci Rev, 8, 2021
7E3J
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BU of 7e3j by Molmil
Crystal structure of SARS-CoV-2 RBD binding to dog ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, ACE2, Spike protein S1, ...
Authors:Zhang, Z, Zhang, Y.
Deposit date:2021-02-08
Release date:2021-04-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.99 Å)
Cite:The molecular basis for SARS-CoV-2 binding to dog ACE2.
Nat Commun, 12, 2021
7NX6
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BU of 7nx6 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, COVOX-222 Fab Heavy chain, ...
Authors:Zhou, D, Ren, J, Stuart, D.
Deposit date:2021-03-17
Release date:2021-04-07
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Antibody evasion by the P.1 strain of SARS-CoV-2.
Cell, 184, 2021

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數據於2024-06-12公開中

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