Cryo-EM structure of complement C5 in complex with nanobodies UNbC5-1 and UNbC5-2
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8cml
Q-score: 0.415
Struijf EM, De la O Becerra KI, Ruyken M, de Haas CJC, van Oosterom F, Siere DY, van Keulen JE, Heesterbeek DAC, Dolk E, Heukers R, Bardoel BW, Gros P, Rooijakkers SHM
J Biol Chem (2023) 299 pp. 104956-104956 [ Pubmed: 37356719 DOI: doi:10.1016/j.jbc.2023.104956 ]
- Nanobody unbc5-1 (16 kDa, Protein from Lama glama)
- Nanobody unbc5-2 (16 kDa, Protein from Lama glama)
- Complement c5 bound to nanobodies unbc5-1 and unbc5-2 (218 kDa, Complex from Homo sapiens)
- Complement c5 beta chain (73 kDa, Protein from Homo sapiens)
- Complement c5 alpha chain (112 kDa, Protein from Homo sapiens)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7zw1
Q-score: 0.374
Sci Adv (2022) 8 pp. eadd3677-eadd3677 [ Pubmed: 36351012 DOI: doi:10.1126/sciadv.add3677 ]
- Rod outer segment membrane protein 1 (37 kDa, Protein from Homo sapiens)
- Peripherin-2 (40 kDa, Protein from Homo sapiens)
- Human prph2-rom1 hetero-dimer (Complex from Homo sapiens)
- Human prph2-rom1 hetero-dimer (76 MDa, Complex)
- Nanobody (Complex from Lama)
- Nanobody (14 kDa, Protein from Lama)
Cryo-EM structure of complement C4b in complex with nanobody E3
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 7b2m
Q-score: 0.445
De la O Becerra KI, Oosterheert W, van den Bos RM, Xenaki KT, Lorent JH, Ruyken M, Schouten A, Rooijakkers SHM, van Bergen En Henegouwen PMP, Gros P
J Immunol. (2022) 208 pp. 2207-2219 [ DOI: doi:10.4049/jimmunol.2100647 Pubmed: 35428691 ]
- Complement c4 gamma chain (33 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Complement c4 gamma chain (33 kDa, Protein from Homo sapiens)
- Complement c4 alpha chain (84 kDa, Complex from Homo sapiens)
- Complement c4 beta chain (72 kDa, Complex from Homo sapiens)
- Complement c4 alpha chain (84 kDa, Protein from Homo sapiens)
- Complement c4b bound to nanobody e3 (203 kDa, Complex)
- Anti-c4b nanobody e3 (14 kDa, Protein from Lama glama)
- Nanobody e3 (14 kDa, Complex from Lama glama)
- Complement c4 beta chain (71 kDa, Protein from Homo sapiens)
Cryo-EM structure of complement C4b in complex with nanobody B5
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 7b2p
Q-score: 0.411
De la O Becerra KI, Oosterheert W, van den Bos RM, Xenaki KT, Lorent JH, Ruyken M, Schouten A, Rooijakkers SHM, van Bergen En Henegouwen PMP, Gros P
J Immunol. (2022) 208 pp. 2207-2219 [ DOI: doi:10.4049/jimmunol.2100647 Pubmed: 35428691 ]
- Complement c4 gamma chain (33 kDa, Complex from Homo sapiens)
- Complement c4b bound to nanobody b5 (204 kDa, Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Complement c4 gamma chain (33 kDa, Protein from Homo sapiens)
- Complement c4 alpha chain (84 kDa, Complex from Homo sapiens)
- Complement c4 beta chain (72 kDa, Complex from Homo sapiens)
- Nanobody b5 (15 kDa, Complex from Lama glama)
- Complement c4 alpha chain (84 kDa, Protein from Homo sapiens)
- Nanobody b5 (15 kDa, Protein from Lama glama)
- Complement c4 beta chain (71 kDa, Protein from Homo sapiens)
Cryo-EM structure of complement C4b in complex with nanobody B12
Resolution: 3.76 Å
EM Method: Single-particle
Fitted PDBs: 7b2q
Q-score: 0.371
De la O Becerra KI, Oosterheert W, van den Bos RM, Xenaki KT, Lorent JH, Ruyken M, Schouten A, Rooijakkers SHM, van Bergen En Henegouwen PMP, Gros P
J Immunol. (2022) 208 pp. 2207-2219 [ DOI: doi:10.4049/jimmunol.2100647 Pubmed: 35428691 ]
- Complement c4 gamma chain (33 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Complement c4 gamma chain (33 kDa, Protein from Homo sapiens)
- Anti-c4b nanobody b12 (15 kDa, Protein from Lama glama)
- Complement c4 alpha chain (84 kDa, Complex from Homo sapiens)
- Complement c4 beta chain (72 kDa, Complex from Homo sapiens)
- Complement c4 alpha chain (84 kDa, Protein from Homo sapiens)
- Nanobody b12 (15 kDa, Complex from Lama glama)
- Complement c4 beta chain (71 kDa, Protein from Homo sapiens)
- Complement c4b bound to nanobody b12 (204 kDa, Complex)
Cryo-EM structure of trimeric human STEAP1 bound to three Fab120.545 fragments
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 6y9b
Q-score: 0.543
J Biol Chem (2020) 295 pp. 9502-9512 [ Pubmed: 32409586 DOI: doi:10.1074/jbc.RA120.013690 ]
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Fab120.545 light chain (24 kDa, Protein from Mus musculus)
- Fab-fragment 1 of antibody mab120.545 (Complex from house mouse)
- Homo-trimeric steap1, chain a, b and c. (Complex from Homo sapiens)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Trimeric human six-transmembrane epithelial antigen of the prostate (steap1) bound to three fab-fragments of antibody mab120.545 (134 kDa, Complex from Homo sapiens)
- Fab120.545 heavy chain (26 kDa, Protein from Mus musculus)
- Fab-fragment 3 of antibody mab120.545 (Complex from Mus musculus)
- Metalloreductase steap1 (44 kDa, Protein from Homo sapiens)
- Fab fragment 2 of antibody mab120.545 (Complex from Mus musculus)
human STEAP4 bound to NADP, FAD, heme and Fe(III)-NTA.
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6hcy
Q-score: 0.549
Oosterheert W, van Bezouwen LS, Rodenburg RNP, Granneman J, Forster F, Mattevi A, Gros P
Nat Commun (2018) 9 pp. 4337-4337 [ DOI: doi:10.1038/s41467-018-06817-7 Pubmed: 30337524 ]
- Metalloreductase steap4 (52 kDa, Protein from Homo sapiens)
- Nadp nicotinamide-adenine-dinucleotide phosphate (743 Da, Ligand)
- (2r)-3-(phosphonooxy)propane-1,2-diyl dihexanoate (368 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Human six-transmembrane epithelial antigen of the prostate 4 (152 kDa, Complex from Homo sapiens)
human STEAP4 bound to NADPH, FAD and heme.
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6hd1
Q-score: 0.435
Oosterheert W, van Bezouwen LS, Rodenburg RNP, Granneman J, Forster F, Mattevi A, Gros P
Nat Commun (2018) 9 pp. 4337-4337 [ DOI: doi:10.1038/s41467-018-06817-7 Pubmed: 30337524 ]
- Metalloreductase steap4 (52 kDa, Protein from Homo sapiens)
- Nadp nicotinamide-adenine-dinucleotide phosphate (743 Da, Ligand)
- (2r)-3-(phosphonooxy)propane-1,2-diyl dihexanoate (368 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Homotrimer of human steap4. (152 kDa, Complex from Homo sapiens)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM reconstruction of C1-IgG1 complex
Resolution: 10.0 Å
EM Method: Single-particle
Fitted PDBs: 6fcz
Q-score: 0.013
Ugurlar D, Howes SC, de Kreuk BJ, Koning RI, de Jong RN, Beurskens FJ, Schuurman J, Koster AJ, Sharp TH, Parren PWHI, Gros P
Science (2018) 359 pp. 794-797 [ DOI: doi:10.1126/science.aao4988 Pubmed: 29449492 ]
- Complement c1q subcomponent subunit c (14 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Complement c1q (Complex from Homo sapiens)
- C1-igg1 complex (Complex)
- Complement c1q subcomponent subunit b (14 kDa, Protein from Homo sapiens)
- Immunoglobulin gamma-1 heavy chain (24 kDa, Protein from Homo sapiens)
- Immunoglobulin gamma-1 (Complex from Homo sapiens)
- Complement c1q subcomponent subunit a (14 kDa, Protein from Homo sapiens)