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 [ DOI: doi:10.1016/j.xcrm.2024.101668 Pubmed: 39094579 ]
- Sc27 fab light chain (11 kDa, Protein from Homo sapiens)
- Sc27 fab heavy chain (14 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike omicron (ba.1) ectodomain trimer in complex with sc27 fab, global refinement (Complex)
- Sars-cov-2 spike omicron (ba.1) ectodomain (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sc27 fab (Complex from Homo sapiens)
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 [ DOI: doi:10.1016/j.xcrm.2024.101668 Pubmed: 39094579 ]
- Sars-cov-2 spike omicron (ba.1) rbd ectodomain dimer-of-trimers in complex with sc27 fabs (Complex)
- Sc27 fab light chain (25 kDa, Protein from Homo sapiens)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sc27 fab heavy chain (27 kDa, Protein from Homo sapiens)
Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '3 up' RBD conformation
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8oyt
Q-score: 0.161
Cornish K, Huo J, Jones L, Sharma P, Thrush JW, Abdelkarim S, Kipar A, Ramadurai S, Weckener M, Mikolajek H, Liu S, Buckle I, Bentley E, Kirby A, Han X, Laidlaw SM, Hill M, Eyssen L, Norman C, Le Bas A, Clarke J, James W, Stewart JP, Carroll M, Naismith JH, Owens RJ
Open Biol (2024) 14 pp. 230252-230252 [ DOI: doi:10.1098/rsob.230252 Pubmed: 38835241 ]
- Complex of stabilised hexapro omicron ba.1 spike trimer with three h6 nanobodies (Complex)
- H6 nanobody (Complex from Lama glama)
- Stabilised hexapro omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein,fibritin (140 kDa, Protein from Tequatrovirus T4)
- H6 nanobody (14 kDa, Protein from Lama glama)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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 [ Pubmed: 38761799 DOI: doi:10.1016/j.xcrm.2024.101577 ]
- Spike protein s2' (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Cab-a17 antibody (fab) (Complex from Enterobacteria phage T4)
- Cab-a17 antibody (variable) (12 kDa, Protein from Homo sapiens)
- 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 [ Pubmed: 38761799 DOI: doi:10.1016/j.xcrm.2024.101577 ]
- Cab-a17 variable light chain (11 kDa, Protein from Homo sapiens)
- Cab-a17 variable heavy-chain (12 kDa, Protein from Homo sapiens)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Complex between fab preparation of cab-a17 and omicron ba.1 spike (Complex 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 [ Pubmed: 38761799 DOI: doi:10.1016/j.xcrm.2024.101577 ]
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cab-a17 antibody (fab) (Complex from Enterobacteria phage T4)
- Sars-cov2 omicron ba.1 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Cab-a17 antibody (hc) (22 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov2 omicron ba.1 spike in complex with cab-a17 antibody (95 kDa, Complex)
- Cab-a17 antibody (lc) (23 kDa, Protein from Homo sapiens)
Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '2 up 1 down' RBD conformation
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8oyu
Q-score: 0.145
Cornish K, Huo J, Jones L, Sharma P, Thrush JW, Abdelkarim S, Kipar A, Ramadurai S, Weckener M, Mikolajek H, Liu S, Buckle I, Bentley E, Kirby A, Han X, Laidlaw SM, Hill M, Eyssen L, Norman C, Le Bas A, Clarke J, James W, Stewart JP, Carroll M, Naismith JH, Owens RJ
Open Biol (2024) 14 pp. 230252-230252 [ DOI: doi:10.1098/rsob.230252 Pubmed: 38835241 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- H6 nanobody (Complex from Lama glama)
- Stabilised hexapro omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein,fibritin (139 kDa, Protein from Enterobacteria phage T4)
- H6 nanobody (13 kDa, Protein from Lama glama)
- Complex of stabilised hexapro omicron ba.1 spike trimer with two h6 nanobodies (Complex)
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 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)
- 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)
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 ]
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ut28k-rd fab light chain (25 kDa, Protein from Homo sapiens)
- 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 protein with ut28k-rd complex (50 kDa, Complex)
- Ut28k-rd fab heavy chain (27 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8b6v
Q-score: 0.45
Marini G, Poland B, Leininger C, Lukoyanova N, Spielbauer D, Barry JK, Altier D, Lum A, Scolaro E, Ortega CP, Yalpani N, Sandahl G, Mabry T, Klever J, Nowatzki T, Zhao JZ, Sethi A, Kassa A, Crane V, Lu AL, Nelson ME, Eswar N, Topf M, Saibil HR
Nat Commun (2023) 14 pp. 4171-4171 [ DOI: doi:10.1038/s41467-023-39891-7 Pubmed: 37443175 ]
- Mpf2ba1 (49 kDa, Protein from Pseudomonas monteilii)
- Magnesium ion (24 Da, Ligand)
- Mpf2ba1 22-mer pre-pore (Complex from Pseudomonas monteilii)