Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9b2c
Q-score: 0.548
Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D
Immunity (2024) 57 pp. 2914-2927.e7 [ Pubmed: 39488210 DOI: doi:10.1016/j.immuni.2024.10.001 ]
- Spike glycoprotein (17 kDa, Protein from Porcine deltacoronavirus)
- Pd33 fab heavy chain (23 kDa, Protein from Mus sp.)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Pd33 fab kappa light chain (24 kDa, Protein from Mus sp.)
- Porcine deltacoronavirus (pdcov) receptor-binding domain bound to the pd33 antibody fab fragment and the kappa light chain nanobody (Complex from Homo sapiens)
- Kappa light chain nanobody (17 kDa, Protein from Lama glama)
PDCoV S trimer bound by three copies of PD41 Fab
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9dez
Q-score: 0.567
Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D
Immunity (2024) 57 pp. 2914- [ Pubmed: 39488210 DOI: doi:10.1016/j.immuni.2024.10.001 ]
- Spike glycoprotein (128 kDa, Protein from Porcine deltacoronavirus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Palmitoleic acid (254 Da, Ligand)
- Pd41 fab variable heavy-chain (13 kDa, Protein from Mus musculus)
- Pd41 fab variable light-chain (11 kDa, Protein from Mus musculus)
- Complex of pdcov s trimer with pd41 fab (530 kDa, Complex from Deltacoronavirus PDCoV/USA/Illinois121/2014)
PDCoV S RBD bound to PD41 Fab (local refinement)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9df0
Q-score: 0.562
Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D
Immunity (2024) 57 pp. 2914- [ Pubmed: 39488210 DOI: doi:10.1016/j.immuni.2024.10.001 ]
- Spike glycoprotein (128 kDa, Protein from Porcine deltacoronavirus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Pd41 fab variable light-chain (11 kDa, Protein from Mus musculus)
- Pd41 fab variable heavy-chain (13 kDa, Protein from Mus musculus)
- Pdcov s rbd complex with pd41 fab (local refinement) (40 kDa, Complex from Deltacoronavirus PDCoV/USA/Illinois121/2014)
PDCoV S SD2018/300 Apo (Class I)
Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D
Immunity (2024) 57 pp. 2914-2927.e7 [ Pubmed: 39488210 DOI: doi:10.1016/j.immuni.2024.10.001 ]
- Pdcov s trimer (387 kDa, Complex from Deltacoronavirus PDCoV/USA/Illinois121/2014)
- Pdcov s protein (Protein from Porcine deltacoronavirus)
PDCoV S SD2018/300 with one PD41 Fab bound (Class II)
Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D
Immunity (2024) 57 pp. 2914-2927.e7 [ Pubmed: 39488210 DOI: doi:10.1016/j.immuni.2024.10.001 ]
- Pdcov spike glycoprotein (Protein from Porcine deltacoronavirus)
- Pd41 fab variable heavy-chain (Protein from Mus musculus)
- Complex of pdcov s trimer with pd41 fab (530 kDa, Complex from Deltacoronavirus PDCoV/USA/Illinois121/2014)
- Pd41 fab variable light-chain (Protein from Mus musculus)
PDCoV S SD2018/300 with one PD41 Fab bound (Class III)
Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D
Immunity (2024) 57 pp. 2914-2927.e7 [ Pubmed: 39488210 DOI: doi:10.1016/j.immuni.2024.10.001 ]
- Pdcov spike glycoprotein (Protein from Porcine deltacoronavirus)
- Pd41 fab variable heavy-chain (Protein from Mus musculus)
- Complex of pdcov s trimer with pd41 fab (530 kDa, Complex from Deltacoronavirus PDCoV/USA/Illinois121/2014)
- Pd41 fab variable light-chain (Protein from Mus musculus)
PDCoV S SD2018/300 with two PD41 Fabs bound (Class IV)
Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D
Immunity (2024) 57 pp. 2914-2927.e7 [ Pubmed: 39488210 DOI: doi:10.1016/j.immuni.2024.10.001 ]
- Pdcov spike glycoprotein (Protein from Porcine deltacoronavirus)
- Pd41 fab variable heavy-chain (Protein from Mus musculus)
- Complex of pdcov s trimer with pd41 fab (530 kDa, Complex from Deltacoronavirus PDCoV/USA/Illinois121/2014)
- Pd41 fab variable light-chain (Protein from Mus musculus)
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- [ Pubmed: 39383863 DOI: doi:10.1016/j.cell.2024.09.026 ]
- 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)
- Spike glycoprotein (141 kDa, Protein from Homo sapiens)
- Vir-7229 fab light chain (11 kDa, Protein from Homo sapiens)
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- [ Pubmed: 39383863 DOI: doi:10.1016/j.cell.2024.09.026 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Ba.2.86 spike glycoprotein in complex with vir-7229 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8fxb
Q-score: 0.469
Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, de Melo GD, Pinto D, Sprouse K, Scheaffer SM, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota Jr E, Zhou J, Farhat N, Bohan D, Noack J, Chen A, Lempp FA, Quispe J, Kergoat L, Larrous F, Cameroni E, Whitener B, Giannini O, Cippa P, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Rosen LE, Schnell G, Czudnochowski N, Benigni F, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Bourhy H, Schmid MA, Purcell LA, Snell G, Lanzavecchia A, Diamond MS, Corti D, Veesler D
Nature (2023) 621 pp. 592-601 [ DOI: doi:10.1038/s41586-023-06487-6 Pubmed: 37648855 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 xbb.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 heavy chain (50 kDa, Protein from Homo sapiens)
- Processed angiotensin-converting enzyme 2 (74 kDa, Protein from Homo sapiens)
- Sars-cov-2 xbb.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 light chain (23 kDa, Protein from Homo sapiens)
- Spike protein s1 (28 kDa, Protein from Severe acute respiratory syndrome coronavirus)