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신종 코로나바이러스 특집 콘텐츠

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코로나 바이러스
코로나 바이러스, 2020. David S. Goodsell @ RCSB PDB에 의한 오리지널 일러스트를 수정

신종 코로나바이러스 감염증 (Novel Coronavirus disease 2019:COVID-19)의 확산이 세계적으로 매우 큰 문제가 되고 있습니다. 시급히 새로운 바이러스(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)를 이해하고 효과적인 약을 개발하기 위해, 신속하게 구조 생물학 연구가 시작되고 있습니다. PDBj는 사용자의 편의를 도모하기 위해 신종 코로나바이러스의 특집 페이지를 제공하고 있습니다. 매주 수요일에 최신 항목이 추가됩니다.

바이러스 단백질에 관한 해설기사는 아래의 「이달의 분자」 페이지를 참조하십시오.

「전체 엔트리」 탭에는, 모든 PDB ID가 포함되어 있습니다. 이용자가 전체의 독립된 엔트리를 검색하고 싶을 때 사용하실 수 있으며, 동일 저자에 의한 그룹등록의 엔트리도 전부 구별되어 있습니다. 「대표구조」 탭에는, 분해능이 가장 높은 대표구조만을 표지하고 있습니다. 아미노산 서열이 100 % 일치하는 PDB 엔트리의 경우, 다른 리간드를 포함하여도 대표구조에는 제외됩니다. 「최신 엔트리」 탭은, 이번주 공개된 가장 최근의 엔트리 입니다.


Created: 2020-09-03 (last edited: more than 1 year ago)2022-09-02
8HQ7
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BU of 8hq7 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron Prototype RBD in complex with fab L4.65 and L5.34
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, fab L4.65, ...
Authors:Gao, G.F, Liu, S.
Deposit date:2022-12-13
Release date:2023-12-20
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HQG
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BU of 8hqg by Molmil
Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with inhibitor YH-53
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Wang, J, Zhang, J, Li, J.
Deposit date:2022-12-13
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with inhibitor YH-53
To Be Published
8HQH
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BU of 8hqh by Molmil
Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with inhibitor YH-53
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zou, X.F, Zhang, J, Li, J.
Deposit date:2022-12-13
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with inhibitor YH-53
To Be Published
8HQI
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BU of 8hqi by Molmil
Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with inhibitor YH-53
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Li, W.W, Zhang, J, Li, J.
Deposit date:2022-12-13
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with inhibitor YH-53
To Be Published
8HQJ
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BU of 8hqj by Molmil
Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with inhibitor YH-53
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Zhang, J, Li, J.
Deposit date:2022-12-13
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with inhibitor YH-53
To Be Published
8HQT
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BU of 8hqt by Molmil
The complex structure of COPI cargo sorting module with SARS-CoV-2 Spike KxHxx sorting motif
Descriptor: Coatomer subunit beta', SARS-CoV-2 Spike KxHxx motif
Authors:Ma, W.F, Nan, Y.N, Yang, M.R, Li, Y.Q.
Deposit date:2022-12-14
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Tighter ER retention of SARS-CoV-2 Omicron spike caused by a constellation of folding disruptive mutations
To Be Published
8HRD
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BU of 8hrd by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, IMCAS74 Fab heavy chain, IMCAS74 Fab light chain, ...
Authors:Zhao, R.C, Wu, L.L, Han, P.
Deposit date:2022-12-15
Release date:2023-12-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.86 Å)
Cite:Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
8HRI
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BU of 8hri by Molmil
SARS-CoV-2 Delta variant spike protein
Descriptor: Spike glycoprotein
Authors:Xu, J, Cheng, H, Liu, N, Wang, H.W.
Deposit date:2022-12-15
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure
To Be Published
8HRJ
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BU of 8hrj by Molmil
SARS-CoV-2 Delta variant spike protein
Descriptor: Spike glycoprotein
Authors:Xu, J, Cheng, H, Liu, N, Wang, H.W.
Deposit date:2022-12-15
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure
To Be Published
8HRK
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BU of 8hrk by Molmil
SARS-CoV-2 Delta S-RBD-ACE2 complex
Descriptor: Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Xu, J, Meng, F, Liu, N, Wang, H.W.
Deposit date:2022-12-15
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure
To Be Published
8HRL
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BU of 8hrl by Molmil
SARS-CoV-2 Delta S-RBD-ACE2
Descriptor: Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Xu, J, Meng, F, Liu, N, Wang, H.W.
Deposit date:2022-12-15
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure
To Be Published
8HSM
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BU of 8hsm by Molmil
CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67
Descriptor: Beta-2-microglobulin, Ig-like domain-containing protein, PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67
To Be Published
8HSO
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BU of 8hso by Molmil
CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.2 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
Descriptor: Beta-2-microglobulin, Ig-like domain-containing protein, PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.2 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
To Be Published
8HSW
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BU of 8hsw by Molmil
CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.1 ANGSTROM
Descriptor: Beta-2-microglobulin, Ig-like domain-containing protein, THR-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.03 Å)
Cite:CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.1 ANGSTROM
To Be Published
8HT1
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BU of 8ht1 by Molmil
CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.4 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
Descriptor: Beta-2-microglobulin, Ig-like domain-containing protein, THR-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.4 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
To Be Published
8HT9
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BU of 8ht9 by Molmil
CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.2 ANGSTROM
Descriptor: Beta-2-microglobulin, GLU-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL, Ig-like domain-containing protein
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.2 ANGSTROM
To Be Published
8Q7S
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BU of 8q7s by Molmil
Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01
Descriptor: 1,2-ETHANEDIOL, 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE, GLYCEROL, ...
Authors:Guttler, T, Aksu, M, Gorlich, D.
Deposit date:2023-08-16
Release date:2023-12-20
Last modified:2024-01-17
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q93
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BU of 8q93 by Molmil
Crystal structure of the SARS-COV-2 RBD with neutralizing-VHHs Re30H02 and Re21D01
Descriptor: Nanobody Re21D01, Nanobody Re30H02, Spike protein S1
Authors:Aksu, M, Guttler, T, Rymarenko, O, Gorlich, D.
Deposit date:2023-08-19
Release date:2023-12-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q94
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BU of 8q94 by Molmil
Crystal structure of The SARS-COV-2 BA.2.75 RBD with neutralizing-VHHs Re32D03 and Ma3B12
Descriptor: Nanobody Ma3B12, Nanobody Re32D03, Spike protein S1
Authors:Aksu, M, Guttler, T, Gorlich, D.
Deposit date:2023-08-19
Release date:2023-12-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q95
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BU of 8q95 by Molmil
Crystal structure of the SARS-CoV-2 BA.1 RBD with neutralizing-VHHs Ma16B06 and Ma3F05
Descriptor: Nanobody Ma16B06, Nanobody Ma3F05, Spike protein S1
Authors:Aksu, M, Rymarenko, O, Guttler, T, Gorlich, D.
Deposit date:2023-08-19
Release date:2023-12-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8UH9
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BU of 8uh9 by Molmil
Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-272
Descriptor: (1R,2S,5S)-N-{(1S,2S)-1-(5-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5, DI(HYDROXYETHYL)ETHER
Authors:Bulut, H, Hayashi, H, Kuwata, N, Tsuji, K, Das, D, Tamamura, H, Mitsuya, H.
Deposit date:2023-10-07
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.067 Å)
Cite:TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir
To Be Published
8XAB
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BU of 8xab by Molmil
Crystal structure of Ubl1 domain of nonstructural protein 3 of SARS-CoV-2
Descriptor: GLYCEROL, Papain-like protease nsp3
Authors:Li, Y, Ke, Z.
Deposit date:2023-12-03
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.49 Å)
Cite:N-terminus of SARS-CoV-2 Nsp3 Interrupts RNA-driven Phase Separation of N Protein by Displacing RNA
To Be Published
7Y3O
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BU of 7y3o by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody BIOLS56
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of BIOLS56, Light chain of BIOLS56, ...
Authors:Rao, X, Gao, F, Wu, Y, Gao, F.
Deposit date:2022-06-11
Release date:2023-12-27
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
8BZN
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BU of 8bzn by Molmil
SARS-CoV-2 non-structural protein 10 (nsp10) variant T102I
Descriptor: CHLORIDE ION, DIMETHYL SULFOXIDE, Replicase polyprotein 1ab, ...
Authors:Wang, H, Rizvi, S.R.A, Dong, D, Lou, J, Wang, Q, Sopipong, W, Najar, F, Agarwal, P.K, Kozielski, F, Haider, S.
Deposit date:2022-12-15
Release date:2023-12-27
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (2.19 Å)
Cite:Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16.
Elife, 12, 2023
8HN4
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BU of 8hn4 by Molmil
Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope QYIKWPWYI
Descriptor: Beta-2-microglobulin, MHC class I antigen, SARS-CoV-2 T-cell epitope QYIKWPWYI
Authors:Deng, S.S, Jin, T.C, Xu, Z.H.
Deposit date:2022-12-07
Release date:2023-12-27
Method:X-RAY DIFFRACTION (2.853 Å)
Cite:Immune escape at SARS- CoV-2 killer T cell epitope
To be published

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