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Conserved Structures and Dynamics in 5-Proximal Regions of Betacoronavirus RNA Genomes
de Moura TR, Purta E, Bernat A, Martin-Cuevas EM, Kurkowska M, Baulin EF, Mukherjee S, Nowak J, Biela AP, Rawski M, Glatt S, Moreno-Herrero F, Bujnicki JM
Nucleic Acids Res (2024) 52 pp. 3419-3432 [ DOI: doi:10.1093/nar/gkae144 Pubmed: 38426934 ]
Prefusion spike of BA.1 with all-RBD-down conformation
To Be Published
Local refined cryo-EM reconstruction of Omicron BA.5 RBD in complex with 8-9D Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8j1t
Q-score: 0.455
Tai W, Yang K, Liu Y, Li R, Feng S, Chai B, Zhuang X, Qi S, Shi H, Liu Z, Lei J, Ma E, Wang W, Tian C, Le T, Wang J, Chen Y, Tian M, Xiang Y, Yu G, Cheng G
Nat Commun (2023) 14 pp. 8042-8042 [ DOI: doi:10.1038/s41467-023-43798-8 Pubmed: 38052844 ]
- 8-9d fab (Complex from Homo sapiens)
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 rbd bound 8-9d fab (22 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- Sars-cov2 omicron ba.5 rbd (Complex)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
- Spike protein (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM reconstruction of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8j1v
Q-score: 0.374
Tai W, Yang K, Liu Y, Li R, Feng S, Chai B, Zhuang X, Qi S, Shi H, Liu Z, Lei J, Ma E, Wang W, Tian C, Le T, Wang J, Chen Y, Tian M, Xiang Y, Yu G, Cheng G
Nat Commun (2023) 14 pp. 8042-8042 [ DOI: doi:10.1038/s41467-023-43798-8 Pubmed: 38052844 ]
- 8-9d fab variable region (Complex from Homo sapiens)
- Sars-cov2 omicron ba.5 spike ectodomain (Complex)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 spike bound 8-9d fab (369 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s2' (123 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8u28
Q-score: 0.464
Nat Methods (2024) 21 pp. 37-40 [ Pubmed: 37973972 DOI: doi:10.1038/s41592-023-02082-9 ]
Zimmermann L, Zhao X, Makroczyova J, Wachsmuth-Melm M, Prasad V, Hensel Z, Bartenschlager R, Chlanda P
Nat Commun (2023) 14 pp. 7894-7894 [ Pubmed: 38036567 DOI: doi:10.1038/s41467-023-43666-5 ]
Zimmermann L, Zhao X, Makroczyova J, Wachsmuth-Melm M, Prasad V, Hensel Z, Bartenschlager R, Chlanda P
Nat Commun (2023) 14 pp. 7894-7894 [ Pubmed: 38036567 DOI: doi:10.1038/s41467-023-43666-5 ]
SARS-CoV-2 S-protein:D614G mutant in 1-up conformation
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8p99
Q-score: 0.343
Gargantilla M, Frances C, Adhav A, Forcada-Nadal A, Martinez-Gualda B, Marti-Mari O, Lopez-Redondo ML, Melero R, Marco-Marin C, Gougeard N, Espinosa C, Rubio-Del-Campo A, Ruiz-Partida R, Hernandez-Sierra MDP, Villamayor-Belinchon L, Bravo J, Llacer JL, Marina A, Rubio V, San-Felix A, Geller R, Perez-Perez MJ
J Med Chem (2023) 66 pp. 10432-10457 [ DOI: doi:10.1021/acs.jmedchem.3c00576 Pubmed: 37471688 ]
SARS-CoV-2 S protein S:D614G mutant in 3-down with binding site of an entry inhibitor
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8p9y
Q-score: 0.117
Gargantilla M, Frances C, Adhav A, Forcada-Nadal A, Martinez-Gualda B, Marti-Mari O, Lopez-Redondo ML, Melero R, Marco-Marin C, Gougeard N, Espinosa C, Rubio-Del-Campo A, Ruiz-Partida R, Hernandez-Sierra MDP, Villamayor-Belinchon L, Bravo J, Llacer JL, Marina A, Rubio V, San-Felix A, Geller R, Perez-Perez MJ
J Med Chem (2023) 66 pp. 10432-10457 [ DOI: doi:10.1021/acs.jmedchem.3c00576 Pubmed: 37471688 ]
- [(2~{s})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{s})-3-[2-(4-nitrophenyl)sulfanyl-1~{h}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{s})-3-[2-(4-nitrophenyl)sulfanyl-1~{h}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{h}-indol-3-yl]propanoyl]oxysodium (1 kDa, Ligand)
- Spike glycoprotein - severe acute respiratory syndrome coronavirus 2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1,spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sodium ion (22 Da, Ligand)
To Be Published