Structure of Covid Spike variant deltaN135 in fully closed form
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8fu7
Q-score: 0.437
Yu X, Juraszek J, Rutten L, Bakkers MJG, Blokland S, Melchers JM, van den Broek NJF, Verwilligen AYW, Abeywickrema P, Vingerhoets J, Neefs JM, Bakhash SAM, Roychoudhury P, Greninger A, Sharma S, Langedijk JPM
PLoS Pathog (2023) 19 pp. e1011308-e1011308 [ Pubmed: 37126534 DOI: doi:10.1371/journal.ppat.1011308 ]
Structure of Covid Spike variant deltaN135 with one erect RBD
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 8fu8
Q-score: 0.457
Yu X, Juraszek J, Rutten L, Bakkers MJG, Blokland S, Melchers JM, van den Broek NJF, Verwilligen AYW, Abeywickrema P, Vingerhoets J, Neefs JM, Bakhash SAM, Roychoudhury P, Greninger A, Sharma S, Langedijk JPM
PLoS Pathog (2023) 19 pp. e1011308-e1011308 [ Pubmed: 37126534 DOI: doi:10.1371/journal.ppat.1011308 ]
Structure of Covid Spike variant deltaN25 with one erect RBD
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 8fu9
Q-score: 0.365
Yu X, Juraszek J, Rutten L, Bakkers MJG, Blokland S, Melchers JM, van den Broek NJF, Verwilligen AYW, Abeywickrema P, Vingerhoets J, Neefs JM, Bakhash SAM, Roychoudhury P, Greninger A, Sharma S, Langedijk JPM
PLoS Pathog (2023) 19 pp. e1011308-e1011308 [ Pubmed: 37126534 DOI: doi:10.1371/journal.ppat.1011308 ]
Cryo-EM structure of SARS-CoV-2 Delta Spike protein in complex with BA7208 and BA7125 fab
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 7xdl
Q-score: 0.5
Wang Y, Yan A, Song D, Dong C, Rao M, Gao Y, Qi R, Ma X, Wang Q, Xu H, Liu H, Han J, Duan M, Liu S, Yu X, Zong M, Feng J, Jiao J, Zhang H, Li M, Yu B, Wang Y, Meng F, Ni X, Li Y, Shen Z, Sun B, Shao X, Zhao H, Zhao Y, Li R, Zhang Y, Du G, Lu J, You C, Jiang H, Zhang L, Wang L, Dou C, Liu Z, Zhao J
Cell Discov (2023) 9 pp. 3-3 [ Pubmed: 36609558 DOI: doi:10.1038/s41421-022-00509-9 ]
- Cryo-em structure of sars-cov-2 delta spike protein in complex with ba7208 and ba7125 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba7125 fab (22 kDa, Protein from Homo sapiens)
- Ba7208 and ba7125 fab (Complex)
- Ba7208 fab (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein (123 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ba7208 fab (13 kDa, Protein from Homo sapiens)
- Sars-cov-2 delta spike protein (Complex from Homo sapiens)
- Ba7125 fab (22 kDa, Protein from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with BA7054 and BA7125 fab (local refinement)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7xcz
Q-score: 0.528
Wang Y, Yan A, Song D, Dong C, Rao M, Gao Y, Qi R, Ma X, Wang Q, Xu H, Liu H, Han J, Duan M, Liu S, Yu X, Zong M, Feng J, Jiao J, Zhang H, Li M, Yu B, Wang Y, Meng F, Ni X, Li Y, Shen Z, Sun B, Shao X, Zhao H, Zhao Y, Li R, Zhang Y, Du G, Lu J, You C, Jiang H, Zhang L, Wang L, Dou C, Liu Z, Zhao J
Cell Discov (2023) 9 pp. 3-3 [ Pubmed: 36609558 DOI: doi:10.1038/s41421-022-00509-9 ]
- Sars-cov-2 delta rbd (Complex from Homo sapiens)
- Cryo-em structure of sars-cov-2 delta rbd in complex with ba7054 and ba7125 fab (local refinement) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba7125 fab (23 kDa, Protein from Homo sapiens)
- Ba7054 fab (23 kDa, Protein from Homo sapiens)
- Ba7054 fab (23 kDa, Protein from Homo sapiens)
- Ba7054 and ba7125 fab (Complex)
- Ba7125 fab (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with BA7208 and BA7125 fab (local refinement)
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7xda
Q-score: 0.526
Wang Y, Yan A, Song D, Dong C, Rao M, Gao Y, Qi R, Ma X, Wang Q, Xu H, Liu H, Han J, Duan M, Liu S, Yu X, Zong M, Feng J, Jiao J, Zhang H, Li M, Yu B, Wang Y, Meng F, Ni X, Li Y, Shen Z, Sun B, Shao X, Zhao H, Zhao Y, Li R, Zhang Y, Du G, Lu J, You C, Jiang H, Zhang L, Wang L, Dou C, Liu Z, Zhao J
Cell Discov (2023) 9 pp. 3-3 [ Pubmed: 36609558 DOI: doi:10.1038/s41421-022-00509-9 ]
- Ba7208 fab (24 kDa, Protein from Homo sapiens)
- Cryo-em structure of sars-cov-2 delta rbd in complex with ba7208 and ba7125 fab (local refinement) (Complex from Homo sapiens)
- Spike glycoprotein (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ba7208 fab (23 kDa, Protein from Homo sapiens)
- Ba7125 fab (23 kDa, Protein from Homo sapiens)
- Ba7125 fab (23 kDa, Protein from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 Omicron Spike protein in complex with BA7208 fab
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 7xdb
Q-score: 0.502
Wang Y, Yan A, Song D, Dong C, Rao M, Gao Y, Qi R, Ma X, Wang Q, Xu H, Liu H, Han J, Duan M, Liu S, Yu X, Zong M, Feng J, Jiao J, Zhang H, Li M, Yu B, Wang Y, Meng F, Ni X, Li Y, Shen Z, Sun B, Shao X, Zhao H, Zhao Y, Li R, Zhang Y, Du G, Lu J, You C, Jiang H, Zhang L, Wang L, Dou C, Liu Z, Zhao J
Cell Discov (2023) 9 pp. 3-3 [ Pubmed: 36609558 DOI: doi:10.1038/s41421-022-00509-9 ]
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba7208 fab (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron spike protein (Complex)
- Ba7208 fab (13 kDa, Protein from Homo sapiens)
- Cryo-em structure of sars-cov-2 omicron spike protein in complex with ba7208 fab (Complex from Homo sapiens)
- Ba7208 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of SARS-CoV-2 Delta Spike protein in complex with BA7054 and BA7125 fab
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7xdk
Q-score: 0.496
Wang Y, Yan A, Song D, Dong C, Rao M, Gao Y, Qi R, Ma X, Wang Q, Xu H, Liu H, Han J, Duan M, Liu S, Yu X, Zong M, Feng J, Jiao J, Zhang H, Li M, Yu B, Wang Y, Meng F, Ni X, Li Y, Shen Z, Sun B, Shao X, Zhao H, Zhao Y, Li R, Zhang Y, Du G, Lu J, You C, Jiang H, Zhang L, Wang L, Dou C, Liu Z, Zhao J
Cell Discov (2023) 9 pp. 3-3 [ Pubmed: 36609558 DOI: doi:10.1038/s41421-022-00509-9 ]
- Spike glycoprotein (123 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ba7054 fab (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryo-em structure of sars-cov-2 delta spike protein in complex with ba7054 and ba7125 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba7125 fab (22 kDa, Protein from Homo sapiens)
- Ba7125 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 delta spike protein (Complex from Homo sapiens)
- Ba7054 and ba7125 fab (Complex)
- Ba7054 fab (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8i6v
Q-score: 0.494
Liu W, Wang J, Comte-Miserez V, Zhang M, Yu X, Chen Q, Jessen HJ, Mayer A, Wu S, Ye S
EMBO J (2023) 42 pp. e113320-e113320 [ Pubmed: 37066886 DOI: doi:10.15252/embj.2022113320 ]
- Vacuolar transporter chaperone complex subunit 4 (83 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Phosphate ion (94 Da, Ligand)
- Vacuolar transporter chaperone complex subunit 1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Vacuolar transporter chaperone 3 complex subunit 3 (96 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Triphosphate (257 Da, Ligand)
- Cryo-em structure of the polyphosphate polymerase vtc complex(vtc4/vtc3/vtc1) (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Manganese (ii) ion (54 Da, Ligand)
- Water (18 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Structure of STING SAVI-related mutant V147L
Resolution: 3.65 Å
EM Method: Single-particle
Fitted PDBs: 8gsz
Q-score: 0.445