Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6
Walker MR, Underwood A, Bjornsson KH, Raghavan SSR, Bassi MR, Binderup A, Pham LV, Ramirez S, Pinholt M, Dagil R, Knudsen AS, Idorn M, Soegaard M, Wang K, Ward AB, Salanti A, Bukh J, Barfod L
Commun Biol (2024) 7 pp. 1239-1239 [ Pubmed: 39354108 DOI: doi:10.1038/s42003-024-06951-7 ]
- Antibody (Complex from Homo sapiens)
- Alphacoronavirus (Complex)
- Spike glycoprotein,fibritin (141 kDa, Protein from Enterobacteria phage T4)
- K501sp6 fv heavy chain (14 kDa, Protein from Homo sapiens)
- Spike glycoprotein with fibritin (Complex from Severe acute respiratory syndrome coronavirus 2)
- K501sp6 fv light chain (14 kDa, Protein from Homo sapiens)
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)
Prefusion RSV F Bound to Lonafarnib and D25 Fab
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 8kg5
Q-score: 0.499
Yang Q, Xue B, Liu F, Lu Y, Tang J, Yan M, Wu Q, Chen R, Zhou A, Liu L, Liu J, Qu C, Wu Q, Fu M, Zhong J, Dong J, Chen S, Wang F, Zhou Y, Zheng J, Peng W, Shang J, Chen X
Signal Transduct Target Ther (2024) 9 pp. 144-144 [ Pubmed: 38853183 DOI: doi:10.1038/s41392-024-01858-5 ]
- D25 light chain (23 kDa, Protein from Homo sapiens)
- Fusion glycoprotein f0,fibritin (64 kDa, Protein from Enterobacteria phage T4)
- 4-{2-[4-(3,10-dibromo-8-chloro-6,11-dihydro-5h-benzo[5,6]cyclohepta[1,2-b]pyridin-11-yl)piperidin-1-yl]-2-oxoethyl}piperidine-1-carboxamide (638 Da, Ligand)
- D25 heavy chain (24 kDa, Protein from Homo sapiens)
- Prefusion rsv f bound to lonafarnib and d25 fab (Complex from Human respiratory syncytial virus A (strain A2))
SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8p5m
Q-score: 0.554
Mandolesi M, Das H, de Vries L, Yang Y, Kim C, Dhinakaran M, Castro Dopico X, Fischbach J, Kim S, Guryleva MV, Adori M, Chernyshev M, Stalmarck A, Hanke L, McInerney GM, Sheward DJ, Corcoran M, Hallberg BM, Murrell B, Karlsson Hedestam GB
Nat Commun (2024) 15 pp. 6338-6338 [ DOI: doi:10.1038/s41467-024-50286-0 Pubmed: 39068149 ]
- Sars-cov-2 spike (rbd) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Mab-23 (heavy chain variable domain) (48 kDa, Protein from Homo sapiens)
- Monoclonal antibody mab-23 (Complex from Enterobacteria phage T4)
- Spike rbd (two molecules) in complex with two fu2 nanobodies (95 kDa, Complex)
- Mab-23 (light chain variable domain) (23 kDa, Protein from Homo sapiens)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 S protein bound to human neutralising antibody UZGENT_G5
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qpr
Q-score: 0.469
Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L
Ebiomedicine (2024) 100 pp. 104960-104960 [ DOI: doi:10.1016/j.ebiom.2023.104960 Pubmed: 38232633 ]
- Igg heavy chain - fab (24 kDa, Protein from Homo sapiens)
- Complex of sars-cov2 s protein (wuhan) and fab fragment of neutralising human antibody uzgent_g5 (Complex)
- Sars-cov2 s protein with fibritin (trimerization) tag (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab fragment of neutralising human antibody uzgent_g5 (Complex from Homo sapiens)
- Igg light chain - fab (22 kDa, Protein from Homo sapiens)
- Spike glycoprotein,fibritin (142 kDa, Protein from Tequatrovirus T4)
SARS-CoV-2 S protein bound to neutralising antibody UZGENT_A3
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8qq0
Q-score: 0.534
Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L
Ebiomedicine (2024) 100 pp. 104960-104960 [ DOI: doi:10.1016/j.ebiom.2023.104960 Pubmed: 38232633 ]
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Complex of sars-cov2 s protein (wuhan) and fab fragment of neutralising human antibody uzgent_a3 (Complex)
- Igg light chain - fab (22 kDa, Protein from Homo sapiens)
- Fab fragment of neutralising human antibody uzgent_a3 (Complex from Homo sapiens)
- Igg heavy chain - fab (24 kDa, Protein from Homo sapiens)
- Sars-cov2 s protein with fibritin (trimerization) tag (Complex from Severe acute respiratory syndrome coronavirus 2)
BA.4/5 SARS-CoV-2 Spike bound to human ACE2 (local)
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8aqs
Q-score: 0.549
Ni D, Turelli P, Beckert B, Nazarov S, Uchikawa E, Myasnikov A, Pojer F, Trono D, Stahlberg H, Lau K
PLoS Pathog (2023) 19 pp. e1011206-e1011206 [ Pubmed: 37018380 DOI: doi:10.1371/journal.ppat.1011206 ]
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba.4/5 sars-cov-2 spike bound to human ace2 (local) (430 kDa, Complex)
- Processed angiotensin-converting enzyme 2 (101 kDa, Protein from Homo sapiens)
- Sars-cov-2 ba.4/5 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Human ace2 (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
Beta SARS-CoV-2 Spike bound to mouse ACE2 (local)
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8aqt
Q-score: 0.212
Ni D, Turelli P, Beckert B, Nazarov S, Uchikawa E, Myasnikov A, Pojer F, Trono D, Stahlberg H, Lau K
PLoS Pathog (2023) 19 pp. e1011206-e1011206 [ Pubmed: 37018380 DOI: doi:10.1371/journal.ppat.1011206 ]
- Beta sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2,ig gamma-2a chain c region, membrane-bound form (101 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Mouse ace2 (Complex from Homo sapiens)
- Beta sars-cov-2 spike bound to mouse ace2 (430 kDa, Complex)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7zr7
Q-score: 0.258
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-42 fab (Complex from Homo sapiens)
- Sars-cov-2 beta spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Omi-42 fab in complex with sars-cov-2 beta spike glycoprotein (Complex)
- Omi-42 light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Omi-42 heavy chain (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein,fibritin (141 kDa, Protein from Tequatrovirus T4)