Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8qtd
Q-score: 0.454
Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
Cell Rep Med (2024) 5 pp. 101553-101553 [ Pubmed: 38723626 DOI: doi:10.1016/j.xcrm.2024.101553 ]
- Spike glycoprotein,fibritin (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Xbb-7 fab light chain (10 kDa, Protein from Homo sapiens)
- Xbb-7 fab heavy chain (14 kDa, Protein from Homo sapiens)
- Ba-2.86 variant sars-cov2 s protein complexed with xbb-7 fab. (Complex)
- Ba.2.86 variant sars-cov2 s protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Xbb-7 fab (Complex from Homo sapiens)
XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8r8k
Q-score: 0.504
Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
Cell Rep Med (2024) 5 pp. 101553-101553 [ Pubmed: 38723626 DOI: doi:10.1016/j.xcrm.2024.101553 ]
- Ba.2.12.1 spike glycoprotein ectodomain (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein,fibritin (142 kDa, Protein from Tequatrovirus T4)
- Xbb-4 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Xbb-4 fab in complex with sars-cov-2 ba.2.12.1 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Xbb-4 fab (Complex from Homo sapiens)
- Xbb-4 fab light chain (23 kDa, Protein from Homo sapiens)
SD1-2 fab in complex with SARS-COV-2 BA.12.1 Spike Glycoprotein.
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8r1c
Q-score: 0.645
Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
Nat Commun (2024) 15 pp. 2734-2734 [ Pubmed: 38548763 DOI: doi:10.1038/s41467-024-46982-6 ]
- Sd1-2 fab light chain (11 kDa, Protein from Homo sapiens)
- Sd1-2 fab in complex with sars-cov-2 ba.2.12.1 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sd1-2 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Ba.2.12.1 spike glycoprotein ectodomain (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sd1-2 fab (Complex from Homo sapiens)
SD1-3 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
Resolution: 2.37 Å
EM Method: Single-particle
Fitted PDBs: 8r1d
Q-score: 0.658
Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
Nat Commun (2024) 15 pp. 2734-2734 [ Pubmed: 38548763 DOI: doi:10.1038/s41467-024-46982-6 ]
- Water (18 Da, Ligand)
- Ba.2.12.1 spike glycoprotein ectodomain (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sd1-3 fab heavy chain (12 kDa, Protein from Homo sapiens)
- Sd1-3 fab light chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- Sd1-3 fab (Complex from Homo sapiens)
- Sd1-3 fab in complex with sars-cov-2 ba.12.1 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
BA.4/5-5 FAB IN COMPLEX WITH SARS-COV-2 BA.4 SPIKE GLYCOPROTEIN
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8cin
Q-score: 0.514
Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
Nat Commun (2024) 15 pp. 2734-2734 [ Pubmed: 38548763 DOI: doi:10.1038/s41467-024-46982-6 ]
- Ba.4/5-5 fab heavy and light chains. (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-coronavirus-2 ba.4 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba.4/5-5 fab light chain (22 kDa, Protein from Homo sapiens)
- Sars-coronavirus-2 ba.4 spike glycoprotein in complex with ba.4/5-5 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba.4/5-5 fab heavy chain (23 kDa, Protein from Homo sapiens)
OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE RBD (local refinement)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7zr8
Q-score: 0.47
Nutalai R, Zhou D, Tuekprakhon A, Ginn HM, Supasa P, Liu C, Huo J, Mentzer AJ, Duyvesteyn HME, Dijokaite-Guraliuc A, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Constantinides B, Webster H, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Crook D, Pollard AJ, Lambe T, Goulder P, Paterson NG, Williams MA, Hall DR, Mongkolsapaya J, Fry EE, Dejnirattisai W, Ren J, Stuart DI, Screaton GR
Cell (2022) 185 pp. 2116-2131.e18 [ DOI: doi:10.1016/j.cell.2022.05.014 Pubmed: 35662412 ]
- Omi-38 fab in complex with sars-cov-2 beta spike glycoprotein (Complex)
- Omi-38 fab (Complex from Homo sapiens)
- Spike glycoprotein,fibritin (141 kDa, Protein from Enterobacteria phage T4)
- Omi-38 fab heavy chain (12 kDa, Protein from Homo sapiens)
- Omi-38 fab light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 beta spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
OMI-2 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7zr9
Q-score: 0.259
Nutalai R, Zhou D, Tuekprakhon A, Ginn HM, Supasa P, Liu C, Huo J, Mentzer AJ, Duyvesteyn HME, Dijokaite-Guraliuc A, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Constantinides B, Webster H, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Crook D, Pollard AJ, Lambe T, Goulder P, Paterson NG, Williams MA, Hall DR, Mongkolsapaya J, Fry EE, Dejnirattisai W, Ren J, Stuart DI, Screaton GR
Cell (2022) 185 pp. 2116-2131.e18 [ DOI: doi:10.1016/j.cell.2022.05.014 Pubmed: 35662412 ]
- Omi-2 fab light chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein,fibritin (141 kDa, Protein from Enterobacteria phage T4)
- Omi-2 fab (Complex from Homo sapiens)
- Omi-2 fab heavy chain (14 kDa, Protein from Homo sapiens)
- Omi-2 fab in complex with sars-cov-2 beta spike glycoprotein (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 beta spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7zrc
Q-score: 0.394
Nutalai R, Zhou D, Tuekprakhon A, Ginn HM, Supasa P, Liu C, Huo J, Mentzer AJ, Duyvesteyn HME, Dijokaite-Guraliuc A, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Constantinides B, Webster H, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Crook D, Pollard AJ, Lambe T, Goulder P, Paterson NG, Williams MA, Hall DR, Mongkolsapaya J, Fry EE, Dejnirattisai W, Ren J, Stuart DI, Screaton GR
Cell (2022) 185 pp. 2116-2131.e18 [ DOI: doi:10.1016/j.cell.2022.05.014 Pubmed: 35662412 ]
- Omi-38 fab in complex with sars-cov-2 beta spike glycoprotein (Complex)
- Omi-38 fab (Complex from Homo sapiens)
- Spike glycoprotein,fibritin (141 kDa, Protein from Enterobacteria phage T4)
- Omi-38 fab heavy chain (12 kDa, Protein from Homo sapiens)
- Omi-38 fab light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 beta spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
Beta-53 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7q9m
Q-score: 0.325
Liu C, Zhou D, Nutalai R, Duyvesteyn HME, Tuekprakhon A, Ginn HM, Dejnirattisai W, Supasa P, Mentzer AJ, Wang B, Case JB, Zhao Y, Skelly DT, Chen RE, Johnson SA, Ritter TG, Mason C, Malik T, Temperton N, Paterson NG, Williams MA, Hall DR, Clare DK, Howe A, Goulder PJR, Fry EE, Diamond MS, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
Cell Host Microbe (2022) 30 pp. 53- [ Pubmed: 34921776 DOI: doi:10.1016/j.chom.2021.11.013 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Beta-53 fab light chain (23 kDa, Protein from Homo sapiens)
- Beta-53 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Beta-53 fab in complex with sars-cov-2 beta-spike glycoprotein (475 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Beta-44 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Liu C, Zhou D, Nutalai R, Duyvesteyn HME, Tuekprakhon A, Ginn HM, Dejnirattisai W, Supasa P, Mentzer AJ, Wang B, Case JB, Zhao Y, Skelly DT, Chen RE, Johnson SA, Ritter TG, Mason C, Malik T, Temperton N, Paterson NG, Williams MA, Hall DR, Clare DK, Howe A, Goulder PJR, Fry EE, Diamond MS, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
Cell Host Microbe (2022) 30 pp. 53-68.e12 [ Pubmed: 34921776 DOI: doi:10.1016/j.chom.2021.11.013 ]
- Beta-44 fab in complex with sars-cov-2 beta-spike glycoprotein (475 kDa, Complex)
- Sars-cov-2 spike glycoprotein ectodomain, beta variant (Complex from Severe acute respiratory syndrome coronavirus 2)
- Beta-44 fab light chain (Macromolecule from Homo sapiens)
- Fab (Complex from Homo sapiens)
- Beta-44 fab heavy chain (Macromolecule from Homo sapiens)
- Sars-cov-2 spike glycoprotein ectodomain, beta variant (Macromolecule from Severe acute respiratory syndrome coronavirus 2)