SARS-CoV-2 Spike S2 bound to Fab 54043-5
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8vcr
Q-score: 0.535
Johnson NV, Wall SC, Kramer KJ, Holt CM, Periasamy S, Richardson SI, Manamela NP, Suryadevara N, Andreano E, Paciello I, Pierleoni G, Piccini G, Huang Y, Ge P, Allen JD, Uno N, Shiakolas AR, Pilewski KA, Nargi RS, Sutton RE, Abu-Shmais AA, Parks R, Haynes BF, Carnahan RH, Crowe Jr JE, Montomoli E, Rappuoli R, Bukreyev A, Ross TM, Sautto GA, McLellan JS, Georgiev IS
Structure (2024) 32 pp. 1893- [ Pubmed: 39326419 DOI: doi:10.1016/j.str.2024.08.022 ]
- S2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s2 (65 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Fab 54043-5 (Complex from Homo sapiens)
- 54043-5 fab light chain (23 kDa, Protein from Homo sapiens)
- Trimeric s2 bound to fab 54043-5 (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 54043-5 fab heavy chain (25 kDa, Protein from Homo sapiens)
SARS-CoV-2 spike omicron (BA.1) ectodomain trimer in complex with SC27 Fab, local refinement
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vif
Q-score: 0.545
Voss WN, Mallory MA, Byrne PO, Marchioni JM, Knudson SA, Powers JM, Leist SR, Dadonaite B, Townsend DR, Kain J, Huang Y, Satterwhite E, Castillo IN, Mattocks M, Paresi C, Munt JE, Scobey T, Seeger A, Premkumar L, Bloom JD, Georgiou G, McLellan JS, Baric RS, Lavinder JJ, Ippolito GC
Cell Rep Med (2024) 5 pp. 101668-101668 [ DOI: doi:10.1016/j.xcrm.2024.101668 Pubmed: 39094579 ]
- Sc27 fab light chain (11 kDa, Protein from Homo sapiens)
- Sc27 fab heavy chain (14 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike omicron (ba.1) ectodomain trimer in complex with sc27 fab, global refinement (Complex)
- Sars-cov-2 spike omicron (ba.1) ectodomain (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sc27 fab (Complex from Homo sapiens)
SARS-CoV-2 spike omicron (BA.1) RBD ectodomain dimer-of-trimers in complex with SC27 Fabs
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vke
Q-score: 0.544
Voss WN, Mallory MA, Byrne PO, Marchioni JM, Knudson SA, Powers JM, Leist SR, Dadonaite B, Townsend DR, Kain J, Huang Y, Satterwhite E, Castillo IN, Mattocks M, Paresi C, Munt JE, Scobey T, Seeger A, Premkumar L, Bloom JD, Georgiou G, McLellan JS, Baric RS, Lavinder JJ, Ippolito GC
Cell Rep Med (2024) 5 pp. 101668-101668 [ DOI: doi:10.1016/j.xcrm.2024.101668 Pubmed: 39094579 ]
- Sars-cov-2 spike omicron (ba.1) rbd ectodomain dimer-of-trimers in complex with sc27 fabs (Complex)
- Sc27 fab light chain (25 kDa, Protein from Homo sapiens)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sc27 fab heavy chain (27 kDa, Protein from Homo sapiens)
Cryo-EM structure of CD38 in complex with FTL004
Resolution: 3.86 Å
EM Method: Single-particle
Fitted PDBs: 8il3
Q-score: 0.387
Zhang G, Guo C, Wang Y, Zhang X, Liu S, Qu W, Chen C, Yan L, Yang Z, Zhang Z, Jiang X, Chen X, Liu H, Lai Q, Wei X, Lu Y, Zhao S, Deng H, Wang Y, Yu L, Yu H, Wu Y, Su Z, Chen P, Ren Z, Yu M, Qu F, Luo Y, Gou L, Li Q, Huang Y, Ma F, Yang J
J Hematol Oncol (2022) 15 pp. 177-177 [ DOI: doi:10.1186/s13045-022-01395-0 Pubmed: 36581954 ]
- Heavy chain (22 kDa, Protein from Homo sapiens)
- Light chain (23 kDa, Protein from Homo sapiens)
- Cryo-em structure of cd38 in complex with ftl004 (Complex from Homo sapiens)
- Adp-ribosyl cyclase/cyclic adp-ribose hydrolase 1 (26 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 1 YB9-258 Fab (1 RBD up)
Resolution: 6.21 Å
EM Method: Single-particle
Fitted PDBs: 8hc2
Q-score: 0.154
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Light chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer with one rbd up in complex with one yb9-258 fab (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yb9-258 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 2 YB9-258 Fabs (2 RBD up)
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 8hc3
Q-score: 0.224
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer with two rbd up in complex with two yb9-258 fab (Complex)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yb9-258 fab (Complex from Homo sapiens)
- Heavy chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 wildtype spike trimer (6P) in complex with 3 YB9-258 Fabs and 3 R1-32 Fabs (3 RBD up)
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 8hc4
Q-score: 0.221
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Light chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 wildtype spike trimer with three rbd up in complex with three yb9-258 fab and three r1-32 fab (Complex)
- Yb9-258 fab and r1-32 fab (Complex from Homo sapiens)
- Heavy chain of r1-32 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of r1-32 fab (22 kDa, Protein from Homo sapiens)
- Sars-cov-2 wildtype spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 wildtype S1 in complex with YB9-258 Fab and R1-32 Fab
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 8hc5
Q-score: 0.282
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Heavy chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 wildtype s1 in complex with yb9-258 fab and r1-32 fab (Complex)
- Light chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Yb9-258 fab and r1-32 fab (Complex from Homo sapiens)
- Heavy chain of r1-32 fab (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (75 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of r1-32 fab (22 kDa, Protein from Homo sapiens)
- Sars-cov_2 wildtype s1 (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 4.69 Å
EM Method: Single-particle
Fitted PDBs: 8hc6
Q-score: 0.221
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Spike protein s1 (31 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Light chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Yb13-292 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike (6p) in complex with yb13-292 fab, focused refinement of rbd region (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 4.54 Å
EM Method: Single-particle
Fitted PDBs: 8hc7
Q-score: 0.234
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike trimer with in complex with yb9-258 fab, focused refinement of 2 rbd region (Complex)
- Light chain variable region of yb9-258 (11 kDa, Protein from Homo sapiens)
- Yb9-258 fab (Complex from Homo sapiens)
- Spike protein s1 (58 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Heavy chain variable region of yb9-258 (12 kDa, Protein from Homo sapiens)
- Sars-cov_2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)