COVID-19 featured content

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Coronavirus, 2020. Modified from the original illustration by David S. Goodsell@RCSB PDB

The recent outbreak of the Novel Coronavirus disease (COVID-19) is a serious threat to people all over the world. In order to understand and develop an effective drug against this virus (Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2), structural work on the related proteins has already started and the resultant entries are accumulating in the PDB. PDBj provides a portal page for the COVID-19 related entries for our users. New entries will be added simultaneously with the public release from the wwPDB.

An explanation article covering one of the proteins of this virus is available on the "Molecules of the Month" page below:

The tab "All entries" contains all PDB IDs, in case you want to check all independent entries, including group depositions by the same authors. The "Repr. entries" tab contains only representative PDB entries with the highest resolution, excluding duplicate entries with 100% amino acid sequence identitiy, even if they contain a different ligand. Finally, the "Latest entries" tab contains the latest entries released this week.

Created: 2020-10-28 (last edited: more than 1 year ago)

All entries (4279)Repr. entries (1869)Latest entries (113)

6ZLW

SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit
Descriptor:	18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
Authors:	Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
Deposit date:	2020-07-01
Release date:	2020-07-29
Last modified:	2024-05-01
Method:	ELECTRON MICROSCOPY (2.6 Å)
Cite:	Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 369, 2020

6ZM7

SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex
Descriptor:	18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
Authors:	Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
Deposit date:	2020-07-01
Release date:	2020-07-29
Last modified:	2024-05-01
Method:	ELECTRON MICROSCOPY (2.7 Å)
Cite:	Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 369, 2020

6ZN5

SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2
Descriptor:	18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
Authors:	Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
Deposit date:	2020-07-06
Release date:	2020-07-29
Last modified:	2024-05-01
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 369, 2020

6ZOK

SARS-CoV-2-Nsp1-40S complex, focused on body
Descriptor:	18S ribosomal RNA, 40S ribosomal protein S11, 40S ribosomal protein S13, ...
Authors:	Schubert, K, Karousis, E.D, Jomaa, A, Scaiola, A, Echeverria, B, Gurzeler, L.-A, Leibundgut, M, Thiel, V, Muehlemann, O, Ban, N.
Deposit date:	2020-07-07
Release date:	2020-07-29
Last modified:	2021-02-10
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat.Struct.Mol.Biol., 27, 2020

6ZON

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
Descriptor:	18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
Authors:	Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
Deposit date:	2020-07-07
Release date:	2020-07-29
Last modified:	2024-05-01
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 369, 2020

6ZOW

SARS-CoV-2 spike in prefusion 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, DIMETHYL SULFOXIDE, ...
Authors:	Martinez, M, Marabini, R, Carazo, J.M.
Deposit date:	2020-07-07
Release date:	2020-07-29
Last modified:	2022-12-21
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Iucrj, 7, 2020

6ZP4

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
Descriptor:	18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
Authors:	Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
Deposit date:	2020-07-08
Release date:	2020-07-29
Last modified:	2024-05-01
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 369, 2020

6ZP5

SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed 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, DIMETHYL SULFOXIDE, ...
Authors:	Martinez, M, Marabini, R, Carazo, J.M.
Deposit date:	2020-07-08
Release date:	2020-07-29
Last modified:	2022-12-21
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Iucrj, 7, 2020

6ZP7

SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up open 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, DIMETHYL SULFOXIDE, ...
Authors:	Martinez, M, Marabini, R, Carazo, J.M.
Deposit date:	2020-07-08
Release date:	2020-07-29
Last modified:	2022-12-21
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Iucrj, 7, 2020

6ZSL

Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution
Descriptor:	PHOSPHATE ION, SARS-CoV-2 helicase NSP13, ZINC ION
Authors:	Newman, J.A, Yosaatmadja, Y, Douangamath, A, Arrowsmith, C.H, von Delft, F, Edwards, A, Bountra, C, Gileadi, O.
Deposit date:	2020-07-15
Release date:	2020-07-29
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (1.94 Å)
Cite:	Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Commun, 12, 2021

7C7P

Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir
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, CHLORIDE ION
Authors:	Zeng, R, Qiao, J.X, Wang, Y.F, Li, Y.S, Yao, R, Yang, S.Y, Lei, J.
Deposit date:	2020-05-26
Release date:	2020-07-29
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.74 Å)
Cite:	SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model. Science, 371, 2021

7JFQ

The crystal structure of 3CL MainPro of SARS-CoV-2 with de-oxidized C145
Descriptor:	1,2-ETHANEDIOL, 3C-like proteinase, FORMIC ACID
Authors:	Tan, K, Maltseva, N.I, Welk, L.F, Jedrzejczak, R.P, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-07-17
Release date:	2020-07-29
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.55 Å)
Cite:	The crystal structure of 3CL MainPro of SARS-CoV-2 with de-oxidized C145 To Be Published

6WC1

Peptide-bound SARS-CoV-2 Nsp9 RNA-replicase
Descriptor:	SARS-coV-2 Non-structural protein 9, SULFATE ION
Authors:	Littler, D.R, Gully, B.S, Rossjohn, J.
Deposit date:	2020-03-28
Release date:	2020-08-05
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.4 Å)
Cite:	Identification of a putative peptide-binding site at the dimer interface of the SARS-CoV-2 Nsp9 RNA-replicase. To Be Published

6ZWV

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: 3 Closed RBDs
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:	Ke, Z, Qu, K, Nakane, T, Xiong, X, Cortese, M, Zila, V, Scheres, S.H.W, Briggs, J.A.G.
Deposit date:	2020-07-28
Release date:	2020-08-05
Last modified:	2020-12-30
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature, 588, 2020

7JIR

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder457 inhibitor
Descriptor:	2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide, ACETATE ION, ...
Authors:	Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-07-23
Release date:	2020-08-05
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.09 Å)
Cite:	Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun, 12, 2021

7JIT

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder495 inhibitor
Descriptor:	2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-[(carbamoylcarbamoyl)amino]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ACETATE ION, ...
Authors:	Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-07-23
Release date:	2020-08-05
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.95 Å)
Cite:	Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun, 12, 2021

7JIV

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder530 inhibitor
Descriptor:	2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ACETATE ION, ...
Authors:	Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-07-23
Release date:	2020-08-05
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.05 Å)
Cite:	Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun, 12, 2021

7JIW

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530 inhibitor
Descriptor:	2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, CHLORIDE ION, ...
Authors:	Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-07-23
Release date:	2020-08-05
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.3 Å)
Cite:	Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun, 12, 2021

6XLU

Structure of SARS-CoV-2 spike at pH 4.0
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:	Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
Deposit date:	2020-06-29
Release date:	2020-08-12
Last modified:	2021-12-15
Method:	ELECTRON MICROSCOPY (2.4 Å)
Cite:	Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe, 28, 2020

6XM0

Consensus structure of SARS-CoV-2 spike at pH 5.5
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:	Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
Deposit date:	2020-06-29
Release date:	2020-08-12
Last modified:	2021-12-15
Method:	ELECTRON MICROSCOPY (2.7 Å)
Cite:	Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe, 28, 2020

6XM3

Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1
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:	Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
Deposit date:	2020-06-29
Release date:	2020-08-12
Last modified:	2021-12-15
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe, 28, 2020

6XM4

Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 2
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:	Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
Deposit date:	2020-06-29
Release date:	2020-08-12
Last modified:	2021-12-15
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe, 28, 2020

6ZME

SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex
Descriptor:	18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
Authors:	Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
Deposit date:	2020-07-02
Release date:	2020-08-12
Last modified:	2024-05-01
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 369, 2020

6ZRT

Crystal structure of SARS CoV2 main protease in complex with inhibitor Telaprevir
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, DIMETHYL SULFOXIDE, Main Protease
Authors:	Oerlemans, R, Wang, W, Lunev, S, Domling, A, Groves, M.R.
Deposit date:	2020-07-14
Release date:	2020-08-12
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics. Rsc Med Chem, 12, 2020

6ZRU

Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir
Descriptor:	DIMETHYL SULFOXIDE, Main Protease, boceprevir (bound form)
Authors:	Oerlemans, R, Wang, W, Lunev, S, Domling, A, Groves, M.R.
Deposit date:	2020-07-14
Release date:	2020-08-12
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics. Rsc Med Chem, 12, 2020

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Total results:	4279
Displayed results:	25
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