Cryo-EM structure of E. coli FimH lectin domain bound to Fabs 440-2 and 454-3
Silmon de Monerri NC, Che Y, Lees JA, Jasti J, Wu H, Griffor MC, Kodali S, Hawkins JC, Lypowy J, Ponce C, Curley K, Esadze A, Carcamo J, McLellan T, Keeney D, Illenberger A, Matsuka YV, Shanker S, Chorro L, Gribenko AV, Han S, Anderson AS, Donald RGK
PLoS Pathog (2025) 21 pp. e1012325-e1012325 [ Pubmed: 39970181 DOI: doi:10.1371/journal.ppat.1012325 ]
- 440-2 fab light chain (24 kDa, Protein from Mus musculus)
- 440-2 fab heavy chain (24 kDa, Protein from Mus musculus)
- 445-3 fab heavy chain (24 kDa, Protein from Mus musculus)
- 445-3 fab light chain (23 kDa, Protein from Mus musculus)
- Type 1 fimbrin d-mannose specific adhesin fimh, donor strand complemented with fimg peptide 'triple mutant' (32 kDa, Protein from Escherichia coli)
- Fimh-dsg tm in complex with fabs 440-2 and 445-3 (Complex)
- Fimh-dsg tm (Complex from Escherichia coli)
- Fab 445-3 (Complex from Mus musculus)
- Fab 440-2 (Complex from Mus musculus)
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)
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: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8s9g
Q-score: 0.473
Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, de Melo GD, Pinto D, Sprouse K, Scheaffer SM, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota Jr E, Zhou J, Farhat N, Bohan D, Noack J, Chen A, Lempp FA, Quispe J, Kergoat L, Larrous F, Cameroni E, Whitener B, Giannini O, Cippa P, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Rosen LE, Schnell G, Czudnochowski N, Benigni F, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Bourhy H, Schmid MA, Purcell LA, Snell G, Lanzavecchia A, Diamond MS, Corti D, Veesler D
Nature (2023) 621 pp. 592-601 [ Pubmed: 37648855 DOI: doi:10.1038/s41586-023-06487-6 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (28 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- S309 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Sars-cov-2 bn.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (74 kDa, Protein from Homo sapiens)
- Sars-cov-2 bn.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 fab light chain (23 kDa, Protein from Homo sapiens)
Cryo-EM structure of HIV-1 Env trimer BG505 SOSIP.664 in complex with CD4bs antibody Ab1573
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7tfo
Q-score: 0.359
Yang Z, Dam KA, Bridges MD, Hoffmann MAG, DeLaitsch AT, Gristick HB, Escolano A, Gautam R, Martin MA, Nussenzweig MC, Hubbell WL, Bjorkman PJ
Nat Commun (2022) 13 pp. 732-732 [ DOI: doi:10.1038/s41467-022-28424-3 Pubmed: 35136084 ]
- Bg505 sosip.664 in complex with cd4bs antibody ab1573 (Complex from Macaca mulatta)
- Envelope glycoprotein bg505 sosip.664 - gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein bg505 sosip.664 - gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Cd4 binding site antibody ab1573 - fab heavy chain (24 kDa, Protein from Macaca mulatta)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cd4 binding site antibody ab1573 - fab light chain (23 kDa, Protein from Macaca mulatta)
SARS-CoV-2 S B.1.617.2 delta variant + S2M11 + S2L20 Global Refinement
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 7so9
Q-score: 0.6
McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, De Marco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D
Science (2021) 374 pp. 1621-1626 [ DOI: doi:10.1126/science.abl8506 Pubmed: 34751595 ]
- S2l20 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- S2m11 fab light chain (11 kDa, Protein from Homo sapiens)
- S2l20 fab light chain (11 kDa, Protein from Homo sapiens)
- S2m11 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 s b.1.617.2 delta variant + s2m11 fab + s2l20 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 S NTD B.1.617.2 delta variant + S2L20 Local Refinement
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7soa
Q-score: 0.553
McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, De Marco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D
Science (2021) 374 pp. 1621-1626 [ DOI: doi:10.1126/science.abl8506 Pubmed: 34751595 ]
- S2l20 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Sars-cov-2 s ntd b.1.617.2 delta variant + s2l20 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- S2l20 fab light chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 S B.1.617.1 kappa variant + S309 + S2L20 Global Refinement
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 7sob
Q-score: 0.483
McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, De Marco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D
Science (2021) 374 pp. 1621-1626 [ DOI: doi:10.1126/science.abl8506 Pubmed: 34751595 ]
- S2l20 fab heavy chain (13 kDa, Protein from Homo sapiens)
- S2l20 fab light chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- S309 fab heavy chain (14 kDa, Protein from Homo sapiens)
- S309 fab light chain (10 kDa, Protein from Homo sapiens)
- Sars-cov-2 s b.1.617.1 kappa variant + s309 fab + s2l20 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 S RBD B.1.617.1 kappa variant S309 Local Refinement
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7soc
Q-score: 0.541
McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, De Marco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D
Science (2021) 374 pp. 1621-1626 [ DOI: doi:10.1126/science.abl8506 Pubmed: 34751595 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S309 fab light chain (11 kDa, Protein from Homo sapiens)
- S309 fab heavy chain (14 kDa, Protein from Homo sapiens)
- Sars-cov-2 s rbd b.1.617.1 kappa variant + s309 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)