The Cryo-EM structure of a complex between GAD65 and b96.11 Fab
Resolution: 7.3 Å
EM Method: Single-particle
Fitted PDBs: 7lz6
Q-score: 0.139
Stander SHD, Reboul CF, Le SN, Williams DE, Chandler PG, Costa MGS, Hoke DE, Jimma JDT, Fodor J, Fenalti G, Mannering SI, Porebski BT, Schofield P, Christ D, Buckle M, McGowan S, Elmlund D, Rand KD, Buckle AM
bioRxiv (2024) [ DOI: doi:10.1101/2024.03.18.585568 ]
- B96.11 fab light chain (23 kDa, Protein from Homo sapiens)
- Glutamate decarboxylase 2 (56 kDa, Protein from Homo sapiens)
- B96.11 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Gad65-b96.11 complex (Complex from Homo sapiens)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9asd
Q-score: 0.506
Rosen LE, Tortorici MA, De Marco A, Pinto D, Foreman WB, Taylor AL, Park YJ, Bohan D, Rietz T, Errico JM, Hauser K, Dang HV, Chartron JW, Giurdanella M, Cusumano G, Saliba C, Zatta F, Sprouse KR, Addetia A, Zepeda SK, Brown J, Lee J, Dellota Jr E, Rajesh A, Noack J, Tao Q, DaCosta Y, Tsu B, Acosta R, Subramanian S, de Melo GD, Kergoat L, Zhang I, Liu Z, Guarino B, Schmid MA, Schnell G, Miller JL, Lempp FA, Czudnochowski N, Cameroni E, Whelan SPJ, Bourhy H, Purcell LA, Benigni F, di Iulio J, Pizzuto MS, Lanzavecchia A, Telenti A, Snell G, Corti D, Veesler D, Starr TN
Cell (2024) 187 pp. 7196- [ DOI: doi:10.1016/j.cell.2024.09.026 Pubmed: 39383863 ]
- Vir-7229 fab light chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Homo sapiens)
- Vir-7229 fab heavy chain (13 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba 2.86 rbd - s2v29 complex (local refinement) (Complex from Sarbecovirus)
VIR-7229 Fab fragment bound the BA.2.86 spike trimer (global refinement)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9au2
Q-score: 0.499
Rosen LE, Tortorici MA, De Marco A, Pinto D, Foreman WB, Taylor AL, Park YJ, Bohan D, Rietz T, Errico JM, Hauser K, Dang HV, Chartron JW, Giurdanella M, Cusumano G, Saliba C, Zatta F, Sprouse KR, Addetia A, Zepeda SK, Brown J, Lee J, Dellota Jr E, Rajesh A, Noack J, Tao Q, DaCosta Y, Tsu B, Acosta R, Subramanian S, de Melo GD, Kergoat L, Zhang I, Liu Z, Guarino B, Schmid MA, Schnell G, Miller JL, Lempp FA, Czudnochowski N, Cameroni E, Whelan SPJ, Bourhy H, Purcell LA, Benigni F, di Iulio J, Pizzuto MS, Lanzavecchia A, Telenti A, Snell G, Corti D, Veesler D, Starr TN
Cell (2024) 187 pp. 7196- [ DOI: doi:10.1016/j.cell.2024.09.026 Pubmed: 39383863 ]
- Vir-7229 fab light chain (23 kDa, Protein from Homo sapiens)
- Vir-7229 fab heavy chain (24 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ba.2.86 spike glycoprotein in complex with vir-7229 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
Misson Mindrebo LE, Mindrebo JT, Tran Q, Wilkinson MC, Smith JM, Verma M, Casewell NR, Lander GC, Jardine JG
Toxins (2024) 16 [ Pubmed: 39195771 DOI: doi:10.3390/toxins16080361 ]
- H11 fab heavy chain (23 kDa, Protein from Homo sapiens)
- Zinc metalloproteinase-disintegrin-like ecarin (47 kDa, Protein from Echis carinatus)
- H11 fab light chain (22 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ecarin in complex with neutralizing antibody h11 (Complex from Echis pyramidum leakeyi)
- Calcium ion (40 Da, Ligand)
- Endogenous peptide (613 Da, Protein from Homo sapiens)
SARS-CoV-2 S (C.37 Lambda variant) plus S309, S2L20, and S2X303 Fabs
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8vye
Q-score: 0.433
Magaret CA, Li L, deCamp AC, Rolland M, Juraska M, Williamson BD, Ludwig J, Molitor C, Benkeser D, Luedtke A, Simpkins B, Heng F, Sun Y, Carpp LN, Bai H, Dearlove BL, Giorgi EE, Jongeneelen M, Brandenburg B, McCallum M, Bowen JE, Veesler D, Sadoff J, Gray GE, Roels S, Vandebosch A, Stieh DJ, Le Gars M, Vingerhoets J, Grinsztejn B, Goepfert PA, de Sousa LP, Silva MST, Casapia M, Losso MH, Little SJ, Gaur A, Bekker LG, Garrett N, Truyers C, Van Dromme I, Swann E, Marovich MA, Follmann D, Neuzil KM, Corey L, Greninger AL, Roychoudhury P, Hyrien O, Gilbert PB
Nat Commun (2024) 15 pp. 2175-2175 [ Pubmed: 38467646 DOI: doi:10.1038/s41467-024-46536-w ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S2l20 heavy chain (13 kDa, Protein from Homo sapiens)
- Sars-cov-2 s c.37 (lambda variant) plus s309, s2l20, and s2x303 fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S2l20 light chain (11 kDa, Protein from Homo sapiens)
- S2x303 heavy chain (13 kDa, Protein from Homo sapiens)
- S309 light chain (11 kDa, Protein from Homo sapiens)
- S309 heavy chain (14 kDa, Protein from Homo sapiens)
- S2x303 light chain (11 kDa, Protein from Homo sapiens)
SARS-CoV-2 S NTD (C.37 Lambda variant) plus S2L20 and S2X303 Fabs, local refinement
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8vyf
Q-score: 0.459
Magaret CA, Li L, deCamp AC, Rolland M, Juraska M, Williamson BD, Ludwig J, Molitor C, Benkeser D, Luedtke A, Simpkins B, Heng F, Sun Y, Carpp LN, Bai H, Dearlove BL, Giorgi EE, Jongeneelen M, Brandenburg B, McCallum M, Bowen JE, Veesler D, Sadoff J, Gray GE, Roels S, Vandebosch A, Stieh DJ, Le Gars M, Vingerhoets J, Grinsztejn B, Goepfert PA, de Sousa LP, Silva MST, Casapia M, Losso MH, Little SJ, Gaur A, Bekker LG, Garrett N, Truyers C, Van Dromme I, Swann E, Marovich MA, Follmann D, Neuzil KM, Corey L, Greninger AL, Roychoudhury P, Hyrien O, Gilbert PB
Nat Commun (2024) 15 pp. 2175-2175 [ Pubmed: 38467646 DOI: doi:10.1038/s41467-024-46536-w ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S2l20 heavy chain (13 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S2l20 light chain (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 s c.37 (lambda variant) plus s309, s2l20, and s2x303 fabs. local refinement of ntd with s2l20 and s2x303 fabs. (Complex from Severe acute respiratory syndrome coronavirus 2)
- S2x303 heavy chain (13 kDa, Protein from Homo sapiens)
- S2x303 light chain (11 kDa, Protein from Homo sapiens)
SARS-CoV-2 S RBD (C.37 Lambda variant) plus S309 Fab, local refinement
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vyg
Q-score: 0.395
Magaret CA, Li L, deCamp AC, Rolland M, Juraska M, Williamson BD, Ludwig J, Molitor C, Benkeser D, Luedtke A, Simpkins B, Heng F, Sun Y, Carpp LN, Bai H, Dearlove BL, Giorgi EE, Jongeneelen M, Brandenburg B, McCallum M, Bowen JE, Veesler D, Sadoff J, Gray GE, Roels S, Vandebosch A, Stieh DJ, Le Gars M, Vingerhoets J, Grinsztejn B, Goepfert PA, de Sousa LP, Silva MST, Casapia M, Losso MH, Little SJ, Gaur A, Bekker LG, Garrett N, Truyers C, Van Dromme I, Swann E, Marovich MA, Follmann D, Neuzil KM, Corey L, Greninger AL, Roychoudhury P, Hyrien O, Gilbert PB
Nat Commun (2024) 15 pp. 2175-2175 [ Pubmed: 38467646 DOI: doi:10.1038/s41467-024-46536-w ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 s c.37 (lambda variant) plus s309, s2l20, and s2x303 fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 light chain (11 kDa, Protein from Homo sapiens)
- S309 heavy chain (14 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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 ]
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 rbd bound 8-9d fab (22 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov2 omicron ba.5 rbd (Complex)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- 8-9d fab (Complex 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 ]
- Sars-cov2 omicron ba.5 spike ectodomain (Complex)
- 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)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- Spike protein s2' (123 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 8-9d fab variable region (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
XBB 1.0 RBD bound to P4J15 (Local)
Resolution: 3.85 Å
EM Method: Single-particle
Fitted PDBs: 8pq2
Q-score: 0.481
Fenwick C, Turelli P, Duhoo Y, Lau K, Herate C, Marlin R, Lamrayah M, Campos J, Esteves-Leuenberger L, Farina A, Raclot C, Genet V, Fiscalini F, Cesborn J, Perez L, Dereuddre-Bosquet N, Contreras V, Lheureux K, Relouzat F, Abdelnabi R, Leyssen P, Levy Y, Pojer F, Le Grand R, Trono D, Pantaleo G
J Infect (2023) 87 pp. 524-537 [ Pubmed: 37852477 DOI: doi:10.1016/j.jinf.2023.10.008 ]
- Spike xbb.1 rbd up - p4j15 fab (local) (72 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- P4j15 fragment antigen-binding light chain (11 kDa, Protein from Homo sapiens)
- P4j15 fragment antigen-binding heavy chain (13 kDa, Protein from Homo sapiens)
- Spike protein s2' (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)