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 (4418)代表性結構 (1953)最新條目 (11)

9FGS

SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv41N (focused refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Single Chain fragment scFv41N, Spike glycoprotein,Fibritin
Authors:	Berlinguer, M, Chaves-Sanjuan, A, Milazzo, F.M, Minenkova, O, De Santis, R, Bolognesi, M.
Deposit date:	2024-05-25
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (4 Å)
Cite:	Structure of scFv41N in complex with SARS-CoV-2 Spike protein To Be Published

9FGT

SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76 (focused refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Single chain fragment scFv76, Spike glycoprotein,Fibritin
Authors:	Berlinguer, M, Chaves-Sanjuan, A, Milazzo, F.M, Minenkova, O, De Santis, R, Bolognesi, M.
Deposit date:	2024-05-25
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (3.8 Å)
Cite:	Structure of scFv76 in complex with SARS-CoV-2 Omicron Spike protein To Be Published

9FGU

SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein,Fibritin, 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:	2024-06-12
Method:	ELECTRON MICROSCOPY (4.3 Å)
Cite:	Structure of scFv76-77 in complex with SARS-CoV-2 Omicron Spike protein To Be Published

8C0Y

SARS-CoV2 Omicron BA.1 RBD in complex with CAB-A17 antibody
Descriptor:	CAB-A17 antibody (variable), Spike protein S2'
Authors:	Das, H, Hallberg, B.M.
Deposit date:	2022-12-19
Release date:	2024-06-19
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

8QH0

Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Cv2.3194 Heavy chain, GLYCEROL, ...
Authors:	Fernandez, I, Rey, F.A.
Deposit date:	2023-09-06
Release date:	2024-06-19
Method:	X-RAY DIFFRACTION (1.87 Å)
Cite:	A broadly neutralizing antibody against SARS-CoV-2 Omicron variants To Be Published

8QH1

Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Cv2.3194 heavy chain, IGK@ protein, ...
Authors:	Fernandez, I, Rey, F.A.
Deposit date:	2023-09-06
Release date:	2024-06-19
Method:	X-RAY DIFFRACTION (2.65 Å)
Cite:	Pan-neutralizing antibody isolated from a COVID patient To Be Published

8UKD

SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.5)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:	Zhang, Q.E, Acharya, P.
Deposit date:	2023-10-12
Release date:	2024-06-19
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.5) To Be Published

8XBF

Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with antibody O5C2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, O5C2, heavy chain, ...
Authors:	Hsu, H.F, Wu, M.H, Chang, Y.C, Hsu, S.T.D.
Deposit date:	2023-12-06
Release date:	2024-06-19
Last modified:	2024-06-26
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	Functional and structural investigation of a broadly neutralizing SARS-CoV-2 antibody. JCI Insight, 9, 2024

8XXW

Fab M2-7 complexed with SARS-Cov2 RBD and human ACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, M2-7-Heavy chain, M2-7-Light chain, ...
Authors:	Liu, C, Xie, Y.
Deposit date:	2024-01-19
Release date:	2024-06-19
Method:	ELECTRON MICROSCOPY (3.03 Å)
Cite:	Mosaic RBD nanoparticle elicits immunodominant antibody responses across sarbecoviruses. Cell Rep, 43, 2024

8YB5

SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C6 symmetry)
Descriptor:	Non-structural protein 4, Papain-like protease nsp3
Authors:	Huang, Y.X, Zhong, L.J, Zhang, W.X, Ni, T.
Deposit date:	2024-02-11
Release date:	2024-06-19
Method:	ELECTRON MICROSCOPY (4.2 Å)
Cite:	Molecular Architecture of Coronavirus Double Membrane Vesicle Pore Complex To Be Published

9EOW

The 5-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH
Descriptor:	RNA (29-MER)
Authors:	Wacker, A, Schwalbe, H.
Deposit date:	2024-03-15
Release date:	2024-06-19
Method:	SOLUTION NMR
Cite:	The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH. Nucleic Acids Res., 2024

8T7Y

Structure of SARS CoV-2 main protease in complex with Chymostatin.
Descriptor:	3C-like proteinase nsp5, Chymostatin A (bound form)
Authors:	Terzyan, S, Yarla, N, Rao, C.V, Mooers, B.
Deposit date:	2023-06-21
Release date:	2024-06-26
Method:	X-RAY DIFFRACTION (1.78 Å)
Cite:	Structure of SARS CoV-2 main protease in complex with Chymostatin. to be published

8WHZ

BA.2.86 RBD in complex with hACE2 (local refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Processed angiotensin-converting enzyme 2, ...
Authors:	Yue, C, Liu, P.
Deposit date:	2023-09-23
Release date:	2024-06-26
Method:	ELECTRON MICROSCOPY (3.93 Å)
Cite:	Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity Natl Sci Rev, 2024

8X4Z

BA.2.86 Spike Trimer with ins483V mutation (3 RBD down)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:	Yue, C, Liu, P.
Deposit date:	2023-11-16
Release date:	2024-06-26
Method:	ELECTRON MICROSCOPY (3.49 Å)
Cite:	Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity Natl Sci Rev, 2024

8OYT

Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '3 up' RBD 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, H6 nanobody, ...
Authors:	Weckener, M, Naismith, J.H, Owens, R.J.
Deposit date:	2023-05-05
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (3.8 Å)
Cite:	Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2. Open Biology, 14, 2024

8WHU

Spike Trimer of BA.2.86 in complex with two hACE2s
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Processed angiotensin-converting enzyme 2, ...
Authors:	Yue, C, Liu, P.
Deposit date:	2023-09-23
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity Natl Sci Rev, 2024

8WHV

Spike Trimer of BA.2.86 with three RBDs down
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:	Yue, C, Liu, P.
Deposit date:	2023-09-23
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (3.32 Å)
Cite:	Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity Natl Sci Rev, 2024

8WP8

Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD 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:	Li, L.J, Gu, Y.H, Qi, J.X, Gao, G.F.
Deposit date:	2023-10-09
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (2.89 Å)
Cite:	Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2 To Be Published

8X5Q

SARS-CoV-2 BA.2.75 Spike with K356T mutation (3 RBD down)
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:	Yue, C, Liu, P.
Deposit date:	2023-11-17
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (3.47 Å)
Cite:	Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity Natl Sci Rev, 2024

8XLV

Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P), 1-RBD-up state
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:	Li, L.J, Gu, Y.H, Shi, K.Y, Qi, J.X, Gao, G.F.
Deposit date:	2023-12-26
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (3.07 Å)
Cite:	Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants To Be Published

8XM5

Cryo-EM structure of SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:	Li, L.J, Gu, Y.H, Shi, K.Y, Qi, J.X, Gao, G.F.
Deposit date:	2023-12-27
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (2.61 Å)
Cite:	Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants To Be Published

8XMG

Cryo-EM structure of SARS-CoV-2 Omicron HV.1 spike protein(6P), RBD-closed state
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:	Li, L.J, Gu, Y.H, Shi, K.Y, Qi, J.X, Gao, G.F.
Deposit date:	2023-12-27
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants To Be Published

8XMT

Cryo-EM structure of SARS-CoV-2 Omicron EG.5.1 spike protein(6P), RBD-closed state
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:	Li, L.J, Gu, Y.H, Shi, K.Y, Qi, J.X, Gao, G.F.
Deposit date:	2023-12-28
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (3.31 Å)
Cite:	Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants To Be Published

8XN2

SARS-CoV-2 Omicron EG.5.1 RBD in complex with human ACE2 (local refined from the spike protein)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:	Li, L.J, Gu, Y.H, Shi, K.Y, Qi, J.X, Gao, G.F.
Deposit date:	2023-12-28
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (2.79 Å)
Cite:	Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants To Be Published

8XN3

SARS-CoV-2 Omicron HV.1 RBD in complex with human ACE2 (local refinement from the spike protein)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:	Li, L.J, Gu, Y.H, Shi, K.Y, Qi, J.X, Gao, G.F.
Deposit date:	2023-12-28
Release date:	2024-07-03
Method:	ELECTRON MICROSCOPY (2.64 Å)
Cite:	Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants To Be Published

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