9CXE
 
 | | SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation -C1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Singh, S, Hasan, S.S. | | Deposit date: | 2024-07-31 | | Release date: | 2025-03-05 | | Last modified: | 2025-03-19 | | Method: | ELECTRON MICROSCOPY (2.48 Å) | | Cite: | Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
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9I81
 | | SARS-CoV-2 RdRp bound to a stack of three HeE1-2Tyr molecules | | Descriptor: | N-[8-(cyclohexyloxy)-1-oxo-2-phenyl-1H-pyrido[2,1-b][1,3]benzothiazole-4-carbonyl]-L-tyrosine, Non-structural protein 7, Non-structural protein 8, ... | | Authors: | Kabinger, F, Doze, V, Schmitzova, J, Lidschreiber, M, Dienemann, C, Cramer, P. | | Deposit date: | 2025-02-04 | | Release date: | 2025-03-05 | | Last modified: | 2025-03-26 | | Method: | ELECTRON MICROSCOPY (2.98 Å) | | Cite: | Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr.
Proc.Natl.Acad.Sci.USA, 122, 2025
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8YK4
 | | Structure of SARS-CoV-2 RBD and antibody NT-108 | | Descriptor: | Spike protein S1, antibody NT-108, single chain Fv fragment | | Authors: | Anraku, Y, Kita, S, Onodera, T, Sato, A, Tadokoro, T, Adachi, Y, Ito, S, Suzuki, T, Sasaki, J, Shiwa, N, Iwata, N, Nagata, N, Kazuki, Y, Oshimura, M, Sasaki, M, Orba, Y, Suzuki, T, Sawa, H, Hashiguchi, T, Fukuhara, H, Takahashi, Y, Maenaka, K. | | Deposit date: | 2024-03-04 | | Release date: | 2025-03-12 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structural Basis for Potent Neutralization Activity of SARS-CoV-2 Antibody, NT-108
To Be Published
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8YKG
 | | Structure of SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (1-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, NT-108 scFv, ... | | Authors: | Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K. | | Deposit date: | 2024-03-05 | | Release date: | 2025-03-12 | | Method: | ELECTRON MICROSCOPY (3.28 Å) | | Cite: | Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
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8YKH
 | | Structure of SARS-CoV-2 spike RBD in complex with NT-108 scFv | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NT-108 scFv, Spike glycoprotein | | Authors: | Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K. | | Deposit date: | 2024-03-05 | | Release date: | 2025-03-12 | | Method: | ELECTRON MICROSCOPY (3.27 Å) | | Cite: | Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
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9BLL
 | | Cryo-EM of RBD(EG5.1)/1301B7 Fab Complex | | Descriptor: | 1301B7 Heavy Chain, 1301B7 Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Walter, M.R, Green, T.J. | | Deposit date: | 2024-04-30 | | Release date: | 2025-03-12 | | Method: | ELECTRON MICROSCOPY (4.1 Å) | | Cite: | Potent neutralization by a RBD antibody with broad specificity for SARS-CoV-2 JN.1 and other variants.
Npj Viruses, 2, 2024
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9CCI
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9CCJ
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9CGV
 | | SARS-CoV-2 nsp12 NiRAN domain bound to a covalent inhibitor SW090466-1 | | Descriptor: | MANGANESE (II) ION, Non-structural protein 7, Non-structural protein 8, ... | | Authors: | Osinski, A, Hernandez, G, Tagliabracci, V.S. | | Deposit date: | 2024-07-01 | | Release date: | 2025-03-12 | | Last modified: | 2025-04-23 | | Method: | ELECTRON MICROSCOPY (2.7 Å) | | Cite: | Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine.
J.Biol.Chem., 301, 2025
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9J66
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9N55
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8UTC
 | | HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant) | | Descriptor: | Beta-2-microglobulin, CHLORIDE ION, HLA class I histocompatibility antigen, ... | | Authors: | Oltean, N, Nyovanie, S, Hashem, A, Patskovska, L, Patskovsky, Y, Krogsgaard, M. | | Deposit date: | 2023-10-30 | | Release date: | 2025-03-19 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
To Be Published
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8Z1H
 | | Crystal structure of SARS main protease in complex with PF-00835231 | | Descriptor: | 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide | | Authors: | Lin, C, Zhang, J, Li, J. | | Deposit date: | 2024-04-11 | | Release date: | 2025-03-19 | | Method: | X-RAY DIFFRACTION (2.61 Å) | | Cite: | Crystal structure of SARS main protease in complex with PF-00835231
To Be Published
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9DJ8
 | | RNA-nsp9 bound to the NiRAN domain of the E-RTC with an empty G-pocket | | Descriptor: | ADENOSINE MONOPHOSPHATE, Non-structural protein 9, RNA-directed RNA polymerase, ... | | Authors: | Small, G.I, Darst, S.A, Campbell, E.A. | | Deposit date: | 2024-09-06 | | Release date: | 2025-03-19 | | Last modified: | 2025-10-01 | | Method: | ELECTRON MICROSCOPY (2.58 Å) | | Cite: | The mechanism for GTP-mediated RNA capping by the SARS-CoV-2 NiRAN domain remains unresolved.
Cell, 188, 2025
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9L09
 | | SARS-CoV-2 C-RTC with 13-TP | | Descriptor: | MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ... | | Authors: | Huang, Y.C, Liang, L, Liu, Y.X, Yan, L.M, Lou, Z.Y, Rao, Z.H. | | Deposit date: | 2024-12-12 | | Release date: | 2025-03-19 | | Last modified: | 2025-03-26 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Discovery of a 2'-a-Fluoro-2'-b-C-(fluoromethyl) Purine Nucleotide Prodrug as a Potential Oral Anti-SARS-CoV-2 Agent
J Med Chem, 68, 2025
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9L6C
 | | Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Fab ConD-852, Heavy chain of Fab P2C-1F11, ... | | Authors: | Zheng, Z, Bing, J, Congcong, L, Bing, Z. | | Deposit date: | 2024-12-24 | | Release date: | 2025-03-19 | | Last modified: | 2025-10-01 | | Method: | ELECTRON MICROSCOPY (3.33 Å) | | Cite: | Structure and function of an unusual R452-dependent monoclonal antibody against SARS-CoV-2.
J.Virol., 99, 2025
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8ZYF
 | | Crystal structure of ZW2G10 Fab in complex with omicron RBD | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, ZW2G10 fab heavy chain, ... | | Authors: | Yuan, H.Y, Li, J.M. | | Deposit date: | 2024-06-17 | | Release date: | 2025-03-26 | | Last modified: | 2025-04-16 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Nasal delivery of secretory IgA confers enhanced neutralizing activity against Omicron variants compared to its IgG counterpart.
Mol.Ther., 33, 2025
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9GXE
 | | Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule | | Descriptor: | 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A. | | Deposit date: | 2024-09-30 | | Release date: | 2025-03-26 | | Method: | ELECTRON MICROSCOPY (2.3 Å) | | Cite: | Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
To Be Published
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9GXG
 | | Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule | | Descriptor: | 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone, 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A. | | Deposit date: | 2024-09-30 | | Release date: | 2025-03-26 | | Last modified: | 2025-07-02 | | Method: | ELECTRON MICROSCOPY (1.92 Å) | | Cite: | Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
To Be Published
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8YWE
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8ZFV
 | | Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone | | Descriptor: | Ceftriaxone, DI(HYDROXYETHYL)ETHER, Nucleoprotein, ... | | Authors: | Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P. | | Deposit date: | 2024-05-08 | | Release date: | 2025-04-02 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
J.Struct.Biol., 217, 2025
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9IN1
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9KSH
 | | Crystal structure of SARS-CoV-2 main protease in complex with compound 1 | | Descriptor: | 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-pyridin-3-yl-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione | | Authors: | Zhong, Y, Zhao, L, Zhang, W, Peng, W. | | Deposit date: | 2024-11-29 | | Release date: | 2025-04-02 | | Method: | X-RAY DIFFRACTION (1.91 Å) | | Cite: | Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
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9KSJ
 | | Crystal structure of SARS-CoV-2 main protease in complex with compound 8 | | Descriptor: | 3-[[(6E)-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-[5-(2-methoxyethoxy)pyridin-3-yl]-2,4-bis(oxidanylidene)-1,3,5-triazinan-1-yl]methyl]-4-methyl-benzenecarbonitrile, 3C-like proteinase nsp5 | | Authors: | Zhong, Y, Zhao, L, Zhang, W, Peng, W. | | Deposit date: | 2024-11-29 | | Release date: | 2025-04-02 | | Method: | X-RAY DIFFRACTION (1.67 Å) | | Cite: | Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
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9LBS
 | | Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of ConBA-998, Heavy chain of S304 Fab, ... | | Authors: | Zhang, Z, Ju, B, Liu, C. | | Deposit date: | 2025-01-03 | | Release date: | 2025-04-02 | | Last modified: | 2025-10-22 | | Method: | ELECTRON MICROSCOPY (3.41 Å) | | Cite: | A distinctive IGHV3-66 SARS-CoV-2 neutralizing antibody elicited by primary infection with an Omicron variant.
Structure, 33, 2025
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