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COVID-19特辑

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冠状病毒
冠状病毒,2020. 由David S. Goodsell @ RCSB PDB原图修改

最近爆发的新型冠状病毒传染病(Novel Coronavirus disease 2019: COVID-19)对全世界的人们都构成了严重威胁。 为了尽早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以开发出有效的抗病毒药物,已经有很多科研人員开始了相关蛋白结构的研究,并且将所获得的结构数据存储于PDB。 PDBj为用户提供了COVID-19相关数据一览的门户页面,并将于每周三更新当日新发布的相关数据。

有关该病毒蛋白质的解说,请参见下面的“当月的分子”页面。

“所有结构”标签的页面则逐一罗列了所有的结构数据,包括由同一研究组提交的系列数据群。 “代表性结构”标签的页面精选具有相同氨基酸序列的结构数据中的高分辨率数据,不重复选择具同一氨基酸序列的数据,即使该数据可能包含不同配体。 “最新条目”标签内包含本周新更新数据。


Created: 2020-09-03 (last edited: more than 1 year ago)2020-12-02
8V7W
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BU of 8v7w by Molmil
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
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BU of 8v8e by Molmil
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
8HLC
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BU of 8hlc by Molmil
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
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BU of 8hld by Molmil
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
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BU of 8k67 by Molmil
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
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BU of 8k68 by Molmil
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
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BU of 8k6a by Molmil
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
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BU of 8k6b by Molmil
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
8K6D
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BU of 8k6d by Molmil
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
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BU of 8p5m by Molmil
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
8V4F
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BU of 8v4f by Molmil
Model and map from local refinement of a CAB-A17 - Omicron Ba.1 spike complex
Descriptor: CAB-A17 variable heavy-chain, CAB-A17 variable light chain, Spike protein S1
Authors:Hallberg, B.M, Das, H.
Deposit date:2023-11-29
Release date:2024-06-05
Last modified:2024-07-03
Method:ELECTRON MICROSCOPY (2.68 Å)
Cite:Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies.
Cell Rep Med, 5, 2024
8X0X
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BU of 8x0x by Molmil
Crystal structure of JE-5C in complex with SARS-CoV-2 RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of JE-5C Fab, Light chain of JE-5C Fab, ...
Authors:Mohapatra, A, Chen, X.
Deposit date:2023-11-06
Release date:2024-06-05
Last modified:2024-07-03
Method:X-RAY DIFFRACTION (3.45 Å)
Cite:The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine.
Plos Pathog., 20, 2024
8X0Y
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BU of 8x0y by Molmil
Crystal structure of JM-1A in complex with SARS-CoV-2 RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Heavy chain of JM-1A Fab, ...
Authors:Mohapatra, A, Chen, X.
Deposit date:2023-11-06
Release date:2024-06-05
Last modified:2024-07-03
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine.
Plos Pathog., 20, 2024
8YRO
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BU of 8yro by Molmil
SARS-CoV-2 Delta Spike in complex with JL-8C
Descriptor: JL-8C Heavy Chain, JL-8C Light Chain, Spike glycoprotein
Authors:Nguyen, V.H.T, Chen, X.
Deposit date:2024-03-21
Release date:2024-06-05
Last modified:2024-06-26
Method:ELECTRON MICROSCOPY (3.27 Å)
Cite:The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine.
Plos Pathog., 20, 2024
8YRP
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BU of 8yrp by Molmil
SARS-CoV-2 Delta Spike in complex with JM-1A
Descriptor: JM-1A Heavy Chain, JM-1A Light Chain, Spike glycoprotein
Authors:Nguyen, V.H.T, Chen, X.
Deposit date:2024-03-21
Release date:2024-06-05
Last modified:2024-06-26
Method:ELECTRON MICROSCOPY (3.64 Å)
Cite:The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine.
Plos Pathog., 20, 2024
8YZ5
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BU of 8yz5 by Molmil
SARS-CoV-2 Delta Spike in complex with Fab of JE-5C
Descriptor: Fab heavy chain of JE-5C, Fab light chain of JE-5C, Spike glycoprotein
Authors:Chen, X, Wu, Y.-M.
Deposit date:2024-04-06
Release date:2024-06-05
Last modified:2024-06-26
Method:ELECTRON MICROSCOPY (3.93 Å)
Cite:The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine.
Plos Pathog., 20, 2024
8YZ6
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BU of 8yz6 by Molmil
SARS-CoV-2 Spike (BA.1) in complex with Fab of JH-8B
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 heavy chain of JH-8B, ...
Authors:Chen, X, Wu, Y.-M.
Deposit date:2024-04-06
Release date:2024-06-05
Last modified:2024-06-26
Method:ELECTRON MICROSCOPY (4.55 Å)
Cite:The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine.
Plos Pathog., 20, 2024
9FGR
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BU of 9fgr by Molmil
SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, scFv76-77 single chain fragment
Authors:Berlinguer, M, Chaves-Sanjuan, A, Milazzo, F.M, Minenkova, O, De Santis, R, Bolognesi, M.
Deposit date:2024-05-25
Release date:2024-06-05
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Structure of scFv76-77 in complex with SARS-CoV-2 Spike protein
To Be Published
8JMM
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BU of 8jmm by Molmil
Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution.
Descriptor: 7F3 Fv, GW01 Fv, Spike glycoprotein
Authors:Hao, A, Mao, Q, Chen, Z, Huang, J, Sun, L.
Deposit date:2023-06-05
Release date:2024-06-12
Method:ELECTRON MICROSCOPY (3.75 Å)
Cite:Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution.
To Be Published
8JYS
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BU of 8jys by Molmil
SARS-CoV-2 Spike RBD (dimer) in complex with two 2S-1244 nanobodies
Descriptor: IBT-CoV144 nanobody, Spike protein S1
Authors:Yang, Y, Zhang, C.H.
Deposit date:2023-07-03
Release date:2024-06-12
Last modified:2024-07-10
Method:ELECTRON MICROSCOPY (4.5 Å)
Cite:A novel nanobody broadly neutralizes SARS-CoV-2 via induction of spike trimer dimers conformation.
Exploration (Beijing), 4, 2024
8UIR
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BU of 8uir by Molmil
SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.16)
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, Q.E, Acharya, P.
Deposit date:2023-10-10
Release date:2024-06-12
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.16)
To Be Published
8UK1
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BU of 8uk1 by Molmil
SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer consensus (S-RRAR-Omicron-XBB.1.16)
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, Q.E, Acharya, P.
Deposit date:2023-10-11
Release date:2024-06-12
Method:ELECTRON MICROSCOPY (3 Å)
Cite:SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer consensus (S-RRAR-Omicron-XBB.1.16)
To Be Published
8V0V
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BU of 8v0v by Molmil
SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5)
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, Q.E, Acharya, P.
Deposit date:2023-11-17
Release date:2024-06-12
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5)
To Be Published
8XZD
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BU of 8xzd by Molmil
The structure of fox ACE2 and Omicron BF.7 RBD complex
Descriptor: Angiotensin-converting enzyme, Spike protein S1, ZINC ION
Authors:sun, J.Q.
Deposit date:2024-01-21
Release date:2024-06-12
Method:ELECTRON MICROSCOPY (3.47 Å)
Cite:The structure of fox ACE2 and Omicron BF.7 RBD complex
To Be Published
9AYX
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BU of 9ayx by Molmil
SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5.1)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Zhang, Q.E, Acharya, P.
Deposit date:2024-03-08
Release date:2024-06-12
Method:ELECTRON MICROSCOPY (3 Å)
Cite:SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5.1)
To Be Published

222624

数据于2024-07-17公开中

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