SARS-CoV-2 spike omicron (BA.1) ectodomain trimer in complex with SC27 Fab, global refinement
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 [ Pubmed: 39094579 DOI: doi:10.1016/j.xcrm.2024.101668 ]
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 [ Pubmed: 39094579 DOI: doi:10.1016/j.xcrm.2024.101668 ]
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 [ Pubmed: 39094579 DOI: doi:10.1016/j.xcrm.2024.101668 ]
- Sc27 fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 spike omicron (ba.1) ectodomain (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike omicron (ba.1) ectodomain trimer in complex with sc27 fab, global refinement (Complex)
- Sc27 fab heavy chain (14 kDa, Protein from Homo sapiens)
- Sc27 fab light chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 [ Pubmed: 39094579 DOI: doi:10.1016/j.xcrm.2024.101668 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sc27 fab light chain (25 kDa, Protein from Homo sapiens)
- Sc27 fab heavy chain (27 kDa, Protein from Homo sapiens)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike omicron (ba.1) rbd ectodomain dimer-of-trimers in complex with sc27 fabs (Complex)
SARS-CoV2 Omicron BA.1 RBD in complex with CAB-A17 antibody
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 8c0y
Q-score: 0.491
Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hallberg BM
Cell Rep Med (2024) 5 pp. 101577-101577 [ DOI: doi:10.1016/j.xcrm.2024.101577 Pubmed: 38761799 ]
- Sars-cov-2 omicron rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s2' (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cab-a17 antibody (variable) (12 kDa, Protein from Homo sapiens)
- Cab-a17 antibody (fab) (Complex from Enterobacteria phage T4)
- Sars-cov2 omicron ba.1 spike in complex with cab-a17 antibody (95 kDa, Complex)
- Cab-a17 antibody (variable) (11 kDa, Protein from Homo sapiens)
Model and map from local refinement of a CAB-A17 - Omicron Ba.1 spike complex
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 8v4f
Q-score: 0.513
Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hallberg BM
Cell Rep Med (2024) 5 pp. 101577-101577 [ DOI: doi:10.1016/j.xcrm.2024.101577 Pubmed: 38761799 ]
- Complex between fab preparation of cab-a17 and omicron ba.1 spike (Complex from Homo sapiens)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cab-a17 variable light chain (11 kDa, Protein from Homo sapiens)
- Cab-a17 variable heavy-chain (12 kDa, Protein from Homo sapiens)
SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody
Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 8c2r
Q-score: 0.436
Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hallberg BM
Cell Rep Med (2024) 5 pp. 101577-101577 [ DOI: doi:10.1016/j.xcrm.2024.101577 Pubmed: 38761799 ]
- Cab-a17 antibody (lc) (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cab-a17 antibody (fab) (Complex from Enterobacteria phage T4)
- Sars-cov2 omicron ba.1 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov2 omicron ba.1 spike in complex with cab-a17 antibody (95 kDa, Complex)
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cab-a17 antibody (hc) (22 kDa, Protein from Homo sapiens)
SARS-CoV-2 BA.1 RBD with UT28-RD
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8k5g
Q-score: 0.522
Ozawa T, Ikeda Y, Chen L, Suzuki R, Hoshino A, Noguchi A, Kita S, Anraku Y, Igarashi E, Saga Y, Inasaki N, Taminishi S, Sasaki J, Kirita Y, Fukuhara H, Maenaka K, Hashiguchi T, Fukuhara T, Hirabayashi K, Tani H, Kishi H, Niimi H
Structure (2024) 32 pp. 263-272.e7 [ DOI: doi:10.1016/j.str.2023.12.013 Pubmed: 38228146 ]
- Ut28k-rd fab light chain (25 kDa, Protein from Homo sapiens)
- Sars-cov-2 ba.1 spike protein with ut28k-rd complex (50 kDa, Complex)
- Ut28k-rd fab heavy chain (27 kDa, Protein from Homo sapiens)
- Spike protein s1 (25 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ut28k-rd fab (Complex from Homo sapiens)
- Sars-cov-2 ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 BA.1 spike with UT28-RD
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8k5h
Q-score: 0.497
Ozawa T, Ikeda Y, Chen L, Suzuki R, Hoshino A, Noguchi A, Kita S, Anraku Y, Igarashi E, Saga Y, Inasaki N, Taminishi S, Sasaki J, Kirita Y, Fukuhara H, Maenaka K, Hashiguchi T, Fukuhara T, Hirabayashi K, Tani H, Kishi H, Niimi H
Structure (2024) 32 pp. 263-272.e7 [ DOI: doi:10.1016/j.str.2023.12.013 Pubmed: 38228146 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ut28k-rd fab heavy chain (27 kDa, Protein from Homo sapiens)
- Sars-cov-2 ba.1 spike protein with ut28k-rd complex (50 kDa, Complex)
- Ut28k-rd fab light chain (25 kDa, Protein from Homo sapiens)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ut28k-rd fab (Complex from Homo sapiens)
- Sars-cov-2 ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody Fab 1C3
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8f0g
Q-score: 0.469
Hastie KM, Yu X, Ana-Sosa-Batiz F, Zyla DS, Harkins SS, Hariharan C, Wasserman H, Zandonatti MA, Miller R, Maule E, Kim K, Valentine KM, Shresta S, Saphire EO
Cell Rep (2023) 42 pp. 112421-112421 [ Pubmed: 37083327 DOI: doi:10.1016/j.celrep.2023.112421 ]
- Antibody 1c3 fab light chain (11 kDa, Protein from Homo sapiens)
- Structure of sars-cov-2 omicron ba.1 spike in complex with antibody 1c3 fab (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Antibody 1c3 fab heavy chain,antibody 1c3 fab light chain (Complex from Homo sapiens)
- Antibody 1c3 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (134 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)