The Cryo-EM structure of a complex between GAD65 and b96.11 Fab
Resolution: 7.3 Å
EM Method: Single-particle
Fitted PDBs: 7lz6
Q-score: 0.139
Stander SHD, Reboul CF, Le SN, Williams DE, Chandler PG, Costa MGS, Hoke DE, Jimma JDT, Fodor J, Fenalti G, Mannering SI, Porebski BT, Schofield P, Christ D, Buckle M, McGowan S, Elmlund D, Rand KD, Buckle AM
bioRxiv (2024) [ DOI: doi:10.1101/2024.03.18.585568 ]
- B96.11 fab light chain (23 kDa, Protein from Homo sapiens)
- Glutamate decarboxylase 2 (56 kDa, Protein from Homo sapiens)
- B96.11 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Gad65-b96.11 complex (Complex from Homo sapiens)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9asd
Q-score: 0.506
Rosen LE, Tortorici MA, De Marco A, Pinto D, Foreman WB, Taylor AL, Park YJ, Bohan D, Rietz T, Errico JM, Hauser K, Dang HV, Chartron JW, Giurdanella M, Cusumano G, Saliba C, Zatta F, Sprouse KR, Addetia A, Zepeda SK, Brown J, Lee J, Dellota Jr E, Rajesh A, Noack J, Tao Q, DaCosta Y, Tsu B, Acosta R, Subramanian S, de Melo GD, Kergoat L, Zhang I, Liu Z, Guarino B, Schmid MA, Schnell G, Miller JL, Lempp FA, Czudnochowski N, Cameroni E, Whelan SPJ, Bourhy H, Purcell LA, Benigni F, di Iulio J, Pizzuto MS, Lanzavecchia A, Telenti A, Snell G, Corti D, Veesler D, Starr TN
Cell (2024) 187 pp. 7196- [ DOI: doi:10.1016/j.cell.2024.09.026 Pubmed: 39383863 ]
- Vir-7229 fab light chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Homo sapiens)
- Vir-7229 fab heavy chain (13 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba 2.86 rbd - s2v29 complex (local refinement) (Complex from Sarbecovirus)
VIR-7229 Fab fragment bound the BA.2.86 spike trimer (global refinement)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9au2
Q-score: 0.499
Rosen LE, Tortorici MA, De Marco A, Pinto D, Foreman WB, Taylor AL, Park YJ, Bohan D, Rietz T, Errico JM, Hauser K, Dang HV, Chartron JW, Giurdanella M, Cusumano G, Saliba C, Zatta F, Sprouse KR, Addetia A, Zepeda SK, Brown J, Lee J, Dellota Jr E, Rajesh A, Noack J, Tao Q, DaCosta Y, Tsu B, Acosta R, Subramanian S, de Melo GD, Kergoat L, Zhang I, Liu Z, Guarino B, Schmid MA, Schnell G, Miller JL, Lempp FA, Czudnochowski N, Cameroni E, Whelan SPJ, Bourhy H, Purcell LA, Benigni F, di Iulio J, Pizzuto MS, Lanzavecchia A, Telenti A, Snell G, Corti D, Veesler D, Starr TN
Cell (2024) 187 pp. 7196- [ DOI: doi:10.1016/j.cell.2024.09.026 Pubmed: 39383863 ]
- Vir-7229 fab light chain (23 kDa, Protein from Homo sapiens)
- Vir-7229 fab heavy chain (24 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ba.2.86 spike glycoprotein in complex with vir-7229 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 8tg9
Q-score: 0.495
Dunn ME, Kithcart A, Kim JH, Ho AJ, Franklin MC, Romero Hernandez A, de Hoon J, Botermans W, Meyer J, Jin X, Zhang D, Torello J, Jasewicz D, Kamat V, Garnova E, Liu N, Rosconi M, Pan H, Karnik S, Burczynski ME, Zheng W, Rafique A, Nielsen JB, De T, Verweij N, Pandit A, Locke A, Chalasani N, Melander O, Schwantes-An TH, Baras A, Lotta LA, Musser BJ, Mastaitis J, Devalaraja-Narashimha KB, Rankin AJ, Huang T, Herman G, Olson W, Murphy AJ, Yancopoulos GD, Olenchock BA, Morton L
Nature (2024) 633 pp. 654-661 [ DOI: doi:10.1038/s41586-024-07903-1 Pubmed: 39261724 ]
- Regn5381 fab heavy chain (24 kDa, Protein from Mus musculus)
- Atrial natriuretic peptide receptor 1 (52 kDa, Protein from Homo sapiens)
- Regn5381 fab light chain (23 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Active complex of npr1 ectodomain, anp, and regn5381 fab (Complex from Homo sapiens)
- Atrial natriuretic peptide (3 kDa, Protein from Homo sapiens)
Complex of NPR1 ectodomain and REGN5381 Fab in an active-like state with no ANP bound
Resolution: 3.65 Å
EM Method: Single-particle
Fitted PDBs: 8tga
Q-score: 0.117
Dunn ME, Kithcart A, Kim JH, Ho AJ, Franklin MC, Romero Hernandez A, de Hoon J, Botermans W, Meyer J, Jin X, Zhang D, Torello J, Jasewicz D, Kamat V, Garnova E, Liu N, Rosconi M, Pan H, Karnik S, Burczynski ME, Zheng W, Rafique A, Nielsen JB, De T, Verweij N, Pandit A, Locke A, Chalasani N, Melander O, Schwantes-An TH, Baras A, Lotta LA, Musser BJ, Mastaitis J, Devalaraja-Narashimha KB, Rankin AJ, Huang T, Herman G, Olson W, Murphy AJ, Yancopoulos GD, Olenchock BA, Morton L
Nature (2024) 633 pp. 654-661 [ DOI: doi:10.1038/s41586-024-07903-1 Pubmed: 39261724 ]
- Active-like complex of npr1 ectodomain and regn5381 fab, with no anp present (Complex from Homo sapiens)
- Regn5381 fab heavy chain (24 kDa, Protein from Mus musculus)
- Regn5381 fab light chain (23 kDa, Protein from Mus musculus)
- Atrial natriuretic peptide receptor 1 (52 kDa, Protein from Homo sapiens)
Resolution: 4.41 Å
EM Method: Single-particle
Fitted PDBs: 8c89
Q-score: 0.131
de Campos-Mata L, Trinite B, Modrego A, Tejedor Vaquero S, Pradenas E, Pons-Grifols A, Rodrigo Melero N, Carlero D, Marfil S, Santiago C, Raich-Regue D, Bueno-Carrasco MT, Tarres-Freixas F, Abanco F, Urrea V, Izquierdo-Useros N, Riveira-Munoz E, Ballana E, Perez M, Vergara-Alert J, Segales J, Carolis C, Arranz R, Blanco J, Magri G
Nat Commun (2024) 15 pp. 1051-1051 [ DOI: doi:10.1038/s41467-024-45171-9 Pubmed: 38316751 ]
- Spike protein s2' (23 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Spike glycoprotein rbd (Complex from Severe acute respiratory syndrome coronavirus)
- 17t2 fab light chain (23 kDa, Protein from Homo sapiens)
- 17t2 fab (Complex from Homo sapiens)
- 17t2 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron variant spike trimer in complex with three 17t2 fabs (Complex)
Resolution: 3.77 Å
EM Method: Single-particle
Fitted PDBs: 8dtk
Q-score: 0.437
Malewana RD, Stalls V, May A, Lu X, Martinez DR, Schafer A, Li D, Barr M, Sutherland LL, Lee E, Parks R, Beck WE, Newman A, Bock KW, Minai M, Nagata BM, DeMarco CT, Denny TN, Oguin 3rd TH, Rountree W, Wang Y, Mansouri K, Edwards RJ, Sempowski GD, Eaton A, Muramatsu H, Henderson R, Tam Y, Barbosa C, Tang J, Cain DW, Santra S, Moore IN, Andersen H, Lewis MG, Golding H, Seder R, Khurana S, Montefiori DC, Pardi N, Weissman D, Baric RS, Acharya P, Haynes BF, Saunders KO
bioRxiv (2023) [ DOI: doi:10.1101/2023.12.18.572191 Pubmed: 38187726 ]
- Rbd directed antibody dh1047 in complex with sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Dh1047 fab heavy chain (14 kDa, Protein from Homo sapiens)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Dh1047 fab light chain (12 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8d48
Q-score: 0.449
Bianchini F, Crivelli V, Abernathy ME, Guerra C, Palus M, Muri J, Marcotte H, Piralla A, Pedotti M, De Gasparo R, Simonelli L, Matkovic M, Toscano C, Biggiogero M, Calvaruso V, Svoboda P, Cervantes Rincon T, Fava T, Podesvova L, Shanbhag AA, Celoria A, Sgrignani J, Stefanik M, Honig V, Pranclova V, Michalcikova T, Prochazka J, Guerrini G, Mehn D, Ciabattini A, Abolhassani H, Jarrossay D, Uguccioni M, Medaglini D, Pan-Hammarstrom Q, Calzolai L, Fernandez D, Baldanti F, Franzetti-Pellanda A, Garzoni C, Sedlacek R, Ruzek D, Varani L, Cavalli A, Barnes CO, Robbiani DF
Sci Immunol (2023) 8 pp. eade0958-eade0958 [ Pubmed: 36701425 DOI: doi:10.1126/sciimmunol.ade0958 ]
- Sd1.040 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Spike glycoprotein (139 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sd1.040 fab heavy chain, sd1.040 fab light chain (Complex from Homo sapiens)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sd1.040 fab light chain (24 kDa, Protein from Homo sapiens)
- Sd1.040 fab in complex with sars-cov-2 spike 2p (79 kDa, Complex)
SARS-CoV-2 spike trimer in complex with Fab NE12, ensemble map
Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P
Cell Rep (2022) 41 pp. 111528-111528 [ Pubmed: 36302375 DOI: doi:10.1016/j.celrep.2022.111528 ]
- Sars-cov-2 s6p spike trimer (Protein from Severe acute respiratory syndrome coronavirus 2)
- Ne12 fab heavy chain (Protein from Homo sapiens)
- Ne12 fab light chain (Protein from Homo sapiens)
- Sars-cov-2 s6p spike trimer in complex with fab ne12 (580 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 spike trimer in complex with Fab NE12, local refinement map
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7u9o
Q-score: 0.518
Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P
Cell Rep (2022) 41 pp. 111528-111528 [ Pubmed: 36302375 DOI: doi:10.1016/j.celrep.2022.111528 ]
- Ne12 fab light chain (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike receptor-binding domain in complex with fab ne12 (110 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Ne12 fab heavy chain (24 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)