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

Created: 2020-03-11 (last edited: 3 weeks ago)2020-07-17
Repr. entries (123)All entries (317)New entries (5)
6ZLW
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SARS-COV-2 NSP1 BOUND TO THE HUMAN 40S RIBOSOMAL SUBUNIT
Descriptor:40S ribosomal protein SA, 40S ribosomal protein S3a, 40S ribosomal protein S2, ...
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
Method:ELECTRON MICROSCOPY (2.6 Å)
Cite:Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 2020
6ZOK
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SARS-COV-2-NSP1-40S COMPLEX, FOCUSED ON BODY
Descriptor:18S ribosomal RNA, 40S ribosomal protein SA, 40S ribosomal protein S3a, ...
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
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:SARS-CoV-2-Nsp1-40S, focused on body
To Be Published
6ZOW
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SARS-COV-2 SPIKE IN PREFUSION STATE
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Martinez, M., Marabini, R., Carazo, J.M.
Deposit date:2020-07-07
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.
Biorxiv, 2020
6XQB
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SARS-COV-2 RDRP/RNA COMPLEX
Descriptor:RNA-directed RNA polymerase, Non-structural protein 8, Non-structural protein 7, ...
Authors:Liu, B., Shi, W., Yang, Y.
Deposit date:2020-07-09
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structure of SARS-CoV-2 RdRp/RNA complex at 3.4 Angstroms resolution
To Be Published
6ZBP
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H11-H4 COMPLEX WITH SARS-COV-2
Descriptor:Spike glycoprotein, H11-H4, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Naismith, J.H., Huo, J., Mikolajek, H., Ward, P., Dumoux, M., Owens, R.J., LeBas, A.
Deposit date:2020-06-08
Release date:2020-07-29
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:H11-D4 complex with SARS-CoV-2 RBD
To Be Published
6ZSL
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CRYSTAL STRUCTURE OF THE SARS-COV-2 HELICASE AT 1.94 ANGSTROM RESOLUTION
Descriptor:SARS-CoV-2 helicase NSP13, ZINC ION, PHOSPHATE 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
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution
To Be Published
6ZHD
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H11-H4 BOUND TO SPIKE
Descriptor:Spike glycoprotein,Fibritin, Nanobody H11-H4, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Clare, D.K., Naismith, J.H., Weckener, M., Vogirala, V.K.
Deposit date:2020-06-22
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:H11-H4 bound to Spike
To Be Published
6ZON
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SARS-COV-2 NSP1 BOUND TO A HUMAN 43S PREINITIATION RIBOSOME COMPLEX - STATE 1
Descriptor:40S ribosomal protein SA, 40S ribosomal protein S3a, 40S ribosomal protein S2, ...
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
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 2020
6XM5
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STRUCTURE OF SARS-COV-2 SPIKE AT PH 5.5, ALL RBDS DOWN
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Zhou, T., Tsybovsky, Y., Olia, A., Kwong, P.D.
Deposit date:2020-06-29
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike.
Biorxiv, 2020
6XEZ
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STRUCTURE OF SARS-COV-2 REPLICATION-TRANSCRIPTION COMPLEX BOUND TO NSP13 HELICASE - NSP13(2)-RTC
Descriptor:nsp12, nsp8, nsp7, ...
Authors:Chen, J., Malone, B., Llewellyn, E.C., Campbell, E.A., Darst, S.A.
Deposit date:2020-06-14
Release date:2020-07-29
Last modified:2020-08-05
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.
Biorxiv, 2020
6ZOX
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STRUCTURE OF DISULPHIDE-STABILIZED SARS-COV-2 SPIKE PROTEIN TRIMER (X2 DISULPHIDE-BOND MUTANT, G413C, V987C, SINGLE ARG S1/S2 CLEAVAGE SITE)
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Xiong, X., Qu, K., Scheres, S.H.W., Briggs, J.A.G.
Deposit date:2020-07-08
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3 Å)
Cite:A thermostable, closed, SARS-CoV-2 spike protein trimer.
To Be Published
6ZP0
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STRUCTURE OF SARS-COV-2 SPIKE PROTEIN TRIMER (SINGLE ARG S1/S2 CLEAVAGE SITE) IN CLOSED STATE
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Xiong, X., Qu, K., Scheres, S.H.W., Briggs, J.A.G.
Deposit date:2020-07-08
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3 Å)
Cite:A thermostable, closed, SARS-CoV-2 spike protein trimer.
To Be Published
6XEY
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CRYO-EM STRUCTURE OF THE SARS-COV-2 SPIKE GLYCOPROTEIN BOUND TO FAB 2-4
Descriptor:SARS-CoV-2 spike glycoprotein, 2-4 Heavy Chain, 2-4 Light Chain, ...
Authors:Rapp, M., Shapiro, L., Ho, D.D.
Deposit date:2020-06-14
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3.25 Å)
Cite:Potent Neutralizing Monoclonal Antibodies Directed to Multiple Epitopes on the SARS-CoV-2 Spike.
Biorxiv, 2020
6ZP2
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STRUCTURE OF SARS-COV-2 SPIKE PROTEIN TRIMER (K986P, V987P, SINGLE ARG S1/S2 CLEAVAGE SITE) IN LOCKED STATE
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Xiong, X., Qu, K., Scheres, S.H.W., Briggs, J.A.G.
Deposit date:2020-07-08
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:A thermostable, closed, SARS-CoV-2 spike protein trimer.
To Be Published
6XS6
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SARS-COV-2 SPIKE D614G VARIANT, MINUS RBD
Descriptor:Spike glycoprotein
Authors:Wang, X., Egri, S.B., Dudkina, N., Luban, J., Shen, K.
Deposit date:2020-07-15
Release date:2020-07-22
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Biorxiv, 2020
6ZOJ
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SARS-COV-2-NSP1-40S COMPLEX, COMPOSITE MAP
Descriptor:18S ribosomal RNA, 40S ribosomal protein SA, 40S ribosomal protein S3a, ...
Authors:Schubert, K., Karousis, E.D., Jomaa, A., Scaiola, A., Echeverria, B., Gurzeler, L.-A., Leibundgut, M.L., Thiel, V., Muehlemann, O., Ban, N.
Deposit date:2020-07-07
Release date:2020-07-22
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:SARS-CoV-2-Nsp1-40S complex, composite map
To Be Published
6XR8
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DISTINCT CONFORMATIONAL STATES OF SARS-COV-2 SPIKE PROTEIN
Descriptor:Spike glycoprotein, alpha-D-mannopyranose-(1-4)-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, ...
Authors:Zhang, J., Cai, Y.F., Xiao, T.S., Peng, H.Q., Sterling, S.M., Walsh Jr, R.M., Rawson, S., Volloch, S.R., Chen, B.
Deposit date:2020-07-11
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Distinct conformational states of SARS-CoV-2 spike protein
Science, 2020
6ZOY
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STRUCTURE OF DISULPHIDE-STABILIZED SARS-COV-2 SPIKE PROTEIN TRIMER (X1 DISULPHIDE-BOND MUTANT, S383C, D985C, K986P, V987P, SINGLE ARG S1/S2 CLEAVAGE SITE) IN CLOSED STATE
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Xiong, X., Qu, K., Scheres, S.H.W., Briggs, J.A.G.
Deposit date:2020-07-08
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:A thermostable, closed, SARS-CoV-2 spike protein trimer.
To Be Published
6XOA
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THE CRYSTAL STRUCTURE OF 3CL MAINPRO OF SARS-COV-2 WITH C145S MUTATION
Descriptor:3C-like proteinase, 1,2-ETHANEDIOL
Authors:Tan, K., Maltseva, N.I., Welk, L.F., Jedrzejczak, R.P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-07-06
Release date:2020-07-15
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:The crystal structure of 3CL MainPro of SARS-CoV-2 with C145S mutation
To Be Published
6XKL
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SARS-COV-2 HEXAPRO S ONE RBD UP
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Wrapp, D., Hsieh, C.-L., Goldsmith, J.A., McLellan, J.S.
Deposit date:2020-06-26
Release date:2020-07-15
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3.21 Å)
Cite:Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes.
Biorxiv, 2020
6XC2
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CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX WITH NEUTRALIZING ANTIBODY CC12.1
Descriptor:Spike protein S1, CC12.1 light chain, CC12.1 heavy chain, ...
Authors:Yuan, M., Liu, H., Wu, N.C., Zhu, X., Wilson, I.A.
Deposit date:2020-06-08
Release date:2020-07-08
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (3.112 Å)
Cite:Structural basis of a public antibody response to SARS-CoV-2.
Biorxiv, 2020
6XC7
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CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX WITH ANTIBODIES CC12.3 AND CR3022
Descriptor:Spike protein S1, CR3022 heavy chain, CR3022 light chain, ...
Authors:Yuan, M., Liu, H., Wu, N.C., Zhu, X., Wilson, I.A.
Deposit date:2020-06-08
Release date:2020-07-08
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (2.883 Å)
Cite:Structural basis of a public antibody response to SARS-CoV-2.
Biorxiv, 2020
6ZFO
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ASSOCIATION OF TWO COMPLEXES OF LARGELY STRUCTURALLY DISORDERED SPIKE ECTODOMAIN WITH BOUND EY6A FAB
Descriptor:Spike glycoprotein, EY6A heavy chain, EY6A light chain, ...
Authors:Duyvesteyn, H.M.E., Zhou, D., Zhao, Y., Fry, E.E., Ren, J., Stuart, D.I.
Deposit date:2020-06-17
Release date:2020-07-08
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (4.4 Å)
Cite:Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient
To Be Published
6XC4
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CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX WITH NEUTRALIZING ANTIBODY CC12.3
Descriptor:Spike protein S1, CC12.3 heavy chain, CC12.3 light chain, ...
Authors:Yuan, M., Liu, H., Wu, N.C., Zhu, X., Wilson, I.A.
Deposit date:2020-06-08
Release date:2020-07-08
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (2.341 Å)
Cite:Structural basis of a public antibody response to SARS-CoV-2.
Biorxiv, 2020
6XMK
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1.70 A RESOLUTION STRUCTURE OF SARS-COV-2 3CL PROTEASE IN COMPLEX WITH INHIBITOR 7J
Descriptor:3C-like proteinase, (1S,2S)-2-[(N-{[(4,4-difluorocyclohexyl)methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, TETRAETHYLENE GLYCOL
Authors:Lovell, S., Kashipathy, M.M., Battaile, K.P., Rathnayake, A.D., Zheng, J., Kim, Y., Nguyen, H.N., Chang, K.O., Groutas, W.C.
Deposit date:2020-06-30
Release date:2020-07-08
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Efficacy of post-infection treatment of 3CL Protease in the mouse model of MERS-coronavirus infection
To be published
167327
PDB entries from 2020-08-05