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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
5RMJ
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BU of 5rmj by Molmil
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z68299550
Descriptor: 3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide, Helicase, PHOSPHATE ION, ...
Authors:Newman, J.A, Yosaatmadja, Y, Douangamath, A, Aimon, A, Powell, A.J, Dias, A, Fearon, D, Dunnett, L, Brandao-Neto, J, Krojer, T, Skyner, R, Gorrie-Stone, T, Thompson, W, von Delft, F, Arrowsmith, C.H, Edwards, A, Bountra, C, Gileadi, O.
Deposit date:2020-09-16
Release date:2020-09-30
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Nat Commun, 12, 2021
5RMK
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BU of 5rmk by Molmil
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1273312153
Descriptor: Helicase, N-methyl-1H-indole-7-carboxamide, PHOSPHATE ION, ...
Authors:Newman, J.A, Yosaatmadja, Y, Douangamath, A, Aimon, A, Powell, A.J, Dias, A, Fearon, D, Dunnett, L, Brandao-Neto, J, Krojer, T, Skyner, R, Gorrie-Stone, T, Thompson, W, von Delft, F, Arrowsmith, C.H, Edwards, A, Bountra, C, Gileadi, O.
Deposit date:2020-09-16
Release date:2020-09-30
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Nat Commun, 12, 2021
5RML
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BU of 5rml by Molmil
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z85956652
Descriptor: Helicase, N-(3-chloro-2-methylphenyl)glycinamide, PHOSPHATE ION, ...
Authors:Newman, J.A, Yosaatmadja, Y, Douangamath, A, Aimon, A, Powell, A.J, Dias, A, Fearon, D, Dunnett, L, Brandao-Neto, J, Krojer, T, Skyner, R, Gorrie-Stone, T, Thompson, W, von Delft, F, Arrowsmith, C.H, Edwards, A, Bountra, C, Gileadi, O.
Deposit date:2020-09-16
Release date:2020-09-30
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (2.43 Å)
Cite:Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Nat Commun, 12, 2021
5RMM
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BU of 5rmm by Molmil
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with POB0066
Descriptor: (3S,4R)-1-acetyl-4-phenylpyrrolidine-3-carboxylic acid, Helicase, PHOSPHATE ION, ...
Authors:Newman, J.A, Yosaatmadja, Y, Douangamath, A, Aimon, A, Powell, A.J, Dias, A, Fearon, D, Dunnett, L, Brandao-Neto, J, Krojer, T, Skyner, R, Gorrie-Stone, T, Thompson, W, von Delft, F, Arrowsmith, C.H, Edwards, A, Bountra, C, Gileadi, O.
Deposit date:2020-09-16
Release date:2020-09-30
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Nat Commun, 12, 2021
6ZB4
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BU of 6zb4 by Molmil
SARS CoV-2 Spike protein, Closed conformation, C1 symmetry
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:Toelzer, C, Gupta, K, Yadav, S.K.N, Burucu, U, Schaffitzel, C, Berger, I.
Deposit date:2020-06-06
Release date:2020-09-30
Last modified:2020-11-18
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein.
Science, 370, 2020
6ZB5
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BU of 6zb5 by Molmil
SARS CoV-2 Spike protein, Closed conformation, C3 symmetry
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:Toelzer, C, Gupta, K, Yadav, S.K.N, Burucu, U, Schaffitzel, C, Berger, I.
Deposit date:2020-06-07
Release date:2020-09-30
Last modified:2020-11-18
Method:ELECTRON MICROSCOPY (2.85 Å)
Cite:Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein.
Science, 370, 2020
7A92
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BU of 7a92 by Molmil
Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Unmasked 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:Benton, D.J, Wrobel, A.G, Rosenthal, P.B, Gamblin, S.J.
Deposit date:2020-09-01
Release date:2020-09-30
Last modified:2020-12-16
Method:ELECTRON MICROSCOPY (4.2 Å)
Cite:Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
Nature, 588, 2020
7CWB
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BU of 7cwb by Molmil
Ambient-Temperature Serial Femtosecond X-ray Crystal structure of SARS-CoV-2 Main Protease at 1.9 A Resolution (C121)
Descriptor: 3C-like proteinase
Authors:DeMirci, H.
Deposit date:2020-08-27
Release date:2020-09-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.
Structure, 29, 2021
7CWC
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Ambient-Temperature Serial Femtosecond X-ray Crystal structure of SARS-CoV-2 Main Protease at 2.1 A Resolution (P212121)
Descriptor: 3C-like proteinase
Authors:DeMirci, H.
Deposit date:2020-08-27
Release date:2020-09-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.
Structure, 29, 2021
7K3G
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BU of 7k3g by Molmil
SARS-CoV-2 Envelope Protein Transmembrane Domain: Pentameric Structure Determined by Solid-State NMR
Descriptor: Envelope small membrane protein
Authors:Mandala, V.S, Hong, M, McKay, M.J, Shcherbakov, A.S, Dregni, A.J.
Deposit date:2020-09-11
Release date:2020-09-30
Last modified:2024-05-15
Method:SOLID-STATE NMR
Cite:Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers.
Nat.Struct.Mol.Biol., 27, 2020
7K3N
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BU of 7k3n by Molmil
Crystal Structure of NSP1 from SARS-CoV-2
Descriptor: Host translation inhibitor nsp1
Authors:Semper, C, Watanabe, N, Chang, C, Savchenko, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-09-11
Release date:2020-09-30
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Structural characterization of nonstructural protein 1 from SARS-CoV-2.
Iscience, 24, 2021
7K6D
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SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.48 A Resolution (Cryo-protected)
Descriptor: (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide, 3C-like proteinase, DIMETHYL SULFOXIDE
Authors:Kreitler, D.F, Andi, B, Kumaran, D, Soares, A.S, Shi, W, Jakoncic, J, Fuchs, M.R, Keereetaweep, J, Shanklin, J, McSweeney, S.
Deposit date:2020-09-19
Release date:2020-09-30
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.48 Å)
Cite:Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.
Sci Rep, 12, 2022
7K6E
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SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.63 A Resolution (Direct Vitrification)
Descriptor: (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide, 3C-like proteinase, DIMETHYL SULFOXIDE
Authors:Kreitler, D.F, Andi, B, Kumaran, D, Soares, A.S, Shi, W, Jakoncic, J, Fuchs, M.R, Keereetaweep, J, Shanklin, J, McSweeney, S.
Deposit date:2020-09-19
Release date:2020-09-30
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.63 Å)
Cite:Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.
Sci Rep, 12, 2022
7K7P
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BU of 7k7p by Molmil
Structure of SARS-CoV-2 nonstuctural protein 1
Descriptor: Host translation inhibitor nsp1
Authors:Green, T.J, Petit, C.M, Clark, L.K.
Deposit date:2020-09-23
Release date:2020-09-30
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Structure of Nonstructural Protein 1 from SARS-CoV-2.
J.Virol., 95, 2021
7D3I
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Crystal structure of SARS-CoV-2 main protease in complex with MI-23
Descriptor: (3~{S},3~{a}~{S},6~{a}~{R})-2-[3-[3,5-bis(fluoranyl)phenyl]propanoyl]-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 3C-like proteinase
Authors:Zeng, R, Li, Y.S, Qiao, J.X, Wang, Y.F, Yang, S.Y, Lei, J.
Deposit date:2020-09-19
Release date:2020-10-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.004 Å)
Cite:SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model.
Science, 371, 2021
7D47
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Crystal structure of SARS-CoV-2 Papain-like protease C111S
Descriptor: CALCIUM ION, Non-structural protein 3, ZINC ION
Authors:Wu, K.-P, Chen, S.-K, Lu, Y.-C, Huang, Y.-C.J, Lee, M.-H.
Deposit date:2020-09-22
Release date:2020-10-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.97 Å)
Cite:Crystal structure of SARS-CoV-2 Papain-like protease
To Be Published
7JOY
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BU of 7joy by Molmil
Product structure of SARS-CoV-2 Mpro C145A mutant in complex with its C-terminal autoprocessing sequence.
Descriptor: 3C-like proteinase
Authors:Lee, J, Worrall, L.J, Paetzel, M, Strynadka, N.C.J.
Deposit date:2020-08-07
Release date:2020-10-07
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.
Nat Commun, 11, 2020
7JP1
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Structure of wild-type substrate free SARS-CoV-2 Mpro.
Descriptor: 3C-like proteinase
Authors:Lee, J, Worrall, L.J, Paetzel, M, Strynadka, N.C.J.
Deposit date:2020-08-07
Release date:2020-10-07
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.
Nat Commun, 11, 2020
7JWB
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BU of 7jwb by Molmil
SARS CoV2 Spike ectodomain with engineered trimerized VH binder
Descriptor: Spike glycoprotein, autonomous human heavy chain variable domain
Authors:QCRG Structural Biology Consortium
Deposit date:2020-08-25
Release date:2020-10-07
Last modified:2020-12-30
Method:ELECTRON MICROSCOPY (6 Å)
Cite:Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2.
Nat.Chem.Biol., 17, 2021
7K43
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BU of 7k43 by Molmil
SARS-CoV-2 spike in complex with the S2M11 neutralizing antibody Fab fragment
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2M11 Fab fragment (heavy chain), ...
Authors:Tortorici, M.A, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-14
Release date:2020-10-07
Last modified:2021-01-27
Method:ELECTRON MICROSCOPY (2.6 Å)
Cite:Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.
Science, 370, 2020
7K45
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BU of 7k45 by Molmil
SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment (local refinement of the RBD and Fab variable domains)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2E12 neutralizing antibody Fab fragment (heavy chain), S2E12 neutralizing antibody Fab fragment (light chain), ...
Authors:Tortorici, M.A, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-14
Release date:2020-10-07
Last modified:2023-10-18
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.
Science, 370, 2020
7K4N
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BU of 7k4n by Molmil
SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2E12 neutralizing antibody Fab fragment (heavy chain), ...
Authors:Tortorici, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2020-09-15
Release date:2020-10-07
Last modified:2020-12-02
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.
Science, 370, 2020
6XKP
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BU of 6xkp by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-270
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CV07-270 Heavy Chain, CV07-270 Light Chain, ...
Authors:Liu, H, Yuan, M, Zhu, X, Wu, N.C, Wilson, I.A.
Deposit date:2020-06-26
Release date:2020-10-14
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.72 Å)
Cite:A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.
Cell, 183, 2020
6XKQ
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-250
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CV07-250 Heavy Chain, CV07-250 Light Chain, ...
Authors:Yuan, M, Liu, H, Zhu, X, Wu, N.C, Wilson, I.A.
Deposit date:2020-06-26
Release date:2020-10-14
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.
Cell, 183, 2020
6ZPE
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BU of 6zpe by Molmil
Nonstructural protein 10 (nsp10) from SARS CoV-2
Descriptor: CHLORIDE ION, GLYCEROL, Replicase polyprotein 1ab, ...
Authors:Fisher, S.Z, Kozielski, F.
Deposit date:2020-07-08
Release date:2020-10-14
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2.
Int J Mol Sci, 21, 2020

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