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)
SARS-CoV-2 S/S2M11/S2X333 Local Refinement
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7lxw
Q-score: 0.522
McCallum M, De Marco A, Lempp FA, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Foo SC, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D
Cell (2021) 184 pp. 2332- [ Pubmed: 33761326 DOI: doi:10.1016/j.cell.2021.03.028 ]
- S2x333 fab heavy chain variable region (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 s hexapro bound to s2x333 fab (Complex from Homo sapiens)
- S2x333 fab light chain variable region (10 kDa, Protein from Homo sapiens)
SARS-CoV-2 S/S2M11/S2L28 Local Refinement
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7lxx
Q-score: 0.507
McCallum M, De Marco A, Lempp FA, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Foo SC, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D
Cell (2021) 184 pp. 2332- [ Pubmed: 33761326 DOI: doi:10.1016/j.cell.2021.03.028 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S2l28 fab heavy chain variable region (13 kDa, Protein from Homo sapiens)
- S2l28 fab light chain variable region (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 s hexapro bound to s2l28 fab (Complex from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 S/S2M11/S2X333 Global Refinement
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 7lxy
Q-score: 0.58
McCallum M, De Marco A, Lempp FA, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Foo SC, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D
Cell (2021) 184 pp. 2332- [ Pubmed: 33761326 DOI: doi:10.1016/j.cell.2021.03.028 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 s hexapro bound to s2x333 fab (Complex from Homo sapiens)
- S2x333 fab light chain variable region (10 kDa, Protein from Homo sapiens)
- S2x333 fab heavy chain variable region (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- S2m11 fab heavy chain variable region (13 kDa, Protein from Homo sapiens)
- S2m11 fab light chain variable region (11 kDa, Protein from Homo sapiens)