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 ]
- Complement c5 alpha chain (112 kDa, Protein from Homo sapiens)
- Nanobody unbc5-2 (16 kDa, Protein from Lama glama)
- Nanobody unbc5-1 (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)
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8foz
Q-score: 0.763
O'Neill AG, Burrell AL, Zech M, Elpeleg O, Harel T, Edvardson S, Mor-Shaked H, Rippert AL, Nomakuchi T, Izumi K, Kollman JM
J Biol Chem (2023) 299 pp. 105012-105012 [ Pubmed: 37414152 DOI: doi:10.1016/j.jbc.2023.105012 ]
- Inosinic acid (348 Da, Ligand)
- Inosine-5'-monophosphate dehydrogenase 2 (56 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Filament of inosine-5'-monophosphate dehydrogenase 2 - l245p mutant, bound to atp, imp, and nad+ (Complex from Homo sapiens)
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8fuz
Q-score: 0.735
O'Neill AG, Burrell AL, Zech M, Elpeleg O, Harel T, Edvardson S, Mor-Shaked H, Rippert AL, Nomakuchi T, Izumi K, Kollman JM
J Biol Chem (2023) 299 pp. 105012-105012 [ Pubmed: 37414152 DOI: doi:10.1016/j.jbc.2023.105012 ]
- Inosinic acid (348 Da, Ligand)
- Inosine-5'-monophosphate dehydrogenase 2 (56 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Filament of inosine-5'-monophosphate dehydrogenase 2 - l245p mutant, bound to gtp, atp, imp, and nad+ (Complex from Homo sapiens)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8g8f
Q-score: 0.573
O'Neill AG, Burrell AL, Zech M, Elpeleg O, Harel T, Edvardson S, Mor-Shaked H, Rippert AL, Nomakuchi T, Izumi K, Kollman JM
J Biol Chem (2023) 299 pp. 105012-105012 [ Pubmed: 37414152 DOI: doi:10.1016/j.jbc.2023.105012 ]
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Inosinic acid (348 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Inosine-5'-monophosphate dehydrogenase 2 (56 kDa, Protein from Homo sapiens)
- Filament of inosine-5'-monophosphate dehydrogenase 2 - l245p mutant, bound to atp, imp, and nad+ (Complex from Homo sapiens)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8g9b
Q-score: 0.529
O'Neill AG, Burrell AL, Zech M, Elpeleg O, Harel T, Edvardson S, Mor-Shaked H, Rippert AL, Nomakuchi T, Izumi K, Kollman JM
J Biol Chem (2023) 299 pp. 105012-105012 [ Pubmed: 37414152 DOI: doi:10.1016/j.jbc.2023.105012 ]
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Inosinic acid (348 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Inosine-5'-monophosphate dehydrogenase 2 (56 kDa, Protein from Homo sapiens)
- Filament of inosine-5'-monophosphate dehydrogenase 2 - l245p mutant, bound to gtp, atp, imp, and nad+ (Complex from Homo sapiens)
Mycobacterium tuberculosis ClpC1 hexamer structure
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 8a8u
Q-score: 0.358
Weinhaupl K, Gragera M, Bueno-Carrasco MT, Arranz R, Krandor O, Akopian T, Soares R, Rubin E, Felix J, Fraga H
J Biol Chem (2022) 298 pp. 102553-102553 [ DOI: doi:10.1016/j.jbc.2022.102553 Pubmed: 36208775 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Apo form of mycobacterium tuberculosis clpc1 (567 kDa, Complex from Mycobacterium tuberculosis)
- Atp-dependent clp protease atp-binding subunit clpc1 (94 kDa, Protein from Mycobacterium tuberculosis)
- Bound polypeptide (1 kDa, Protein from Mycobacterium tuberculosis)
Resolution: 3.34 Å
EM Method: Single-particle
Fitted PDBs: 8a8v
Q-score: 0.435
Weinhaupl K, Gragera M, Bueno-Carrasco MT, Arranz R, Krandor O, Akopian T, Soares R, Rubin E, Felix J, Fraga H
J Biol Chem (2022) 298 pp. 102553-102553 [ DOI: doi:10.1016/j.jbc.2022.102553 Pubmed: 36208775 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Mycobacterium tuberculosis clpc1 in complex with the natural product antibiotic cyclomarin (567 kDa, Complex from Mycobacterium tuberculosis)
- Atp-dependent clp protease atp-binding subunit clpc1 (94 kDa, Protein from Mycobacterium tuberculosis)
- Bound polypeptide (1 kDa, Protein from Mycobacterium tuberculosis)
Resolution: 4.29 Å
EM Method: Single-particle
Fitted PDBs: 8a8w
Q-score: 0.266
Weinhaupl K, Gragera M, Bueno-Carrasco MT, Arranz R, Krandor O, Akopian T, Soares R, Rubin E, Felix J, Fraga H
J Biol Chem (2022) 298 pp. 102553-102553 [ DOI: doi:10.1016/j.jbc.2022.102553 Pubmed: 36208775 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Bound polypeptide (2 kDa, Protein from Mycobacterium tuberculosis)
- Atp-dependent clp protease atp-binding subunit clpc1 (94 kDa, Protein from Mycobacterium tuberculosis)
- Mycobacterium tuberculosis clpc1 bound to the natural product antibiotic ecumicin (567 kDa, Complex from Mycobacterium tuberculosis)
Homology model of the full-length AP-3 complex in a compact open conformation
Resolution: 9.1 Å
EM Method: Single-particle
Fitted PDBs: 7p3x
Q-score: 0.085
Schoppe J, Schubert E, Apelbaum A, Yavavli E, Birkholz O, Stephanowitz H, Han Y, Perz A, Hofnagel O, Liu F, Piehler J, Raunser S, Ungermann C
J Biol Chem (2021) 297 pp. 101334-101334 [ DOI: doi:10.1016/j.jbc.2021.101334 Pubmed: 34688652 ]
- Full-length ap-3 complex from saccharomyces cerevisiae (Complex from Saccharomyces cerevisiae)
- Ap complex subunit sigma (21 kDa, Protein from Saccharomyces cerevisiae)
- Ap-3 complex subunit mu (54 kDa, Protein from Saccharomyces cerevisiae)
- Ap-3 complex subunit delta (110 kDa, Protein from Saccharomyces cerevisiae)
- Y55_g0035830.mrna.1.cds.1 (91 kDa, Protein from Saccharomyces cerevisiae)
Homology model of the full-length AP-3 complex in an intermediate open conformation
Resolution: 10.1 Å
EM Method: Single-particle
Fitted PDBs: 7p3y
Q-score: 0.093
Schoppe J, Schubert E, Apelbaum A, Yavavli E, Birkholz O, Stephanowitz H, Han Y, Perz A, Hofnagel O, Liu F, Piehler J, Raunser S, Ungermann C
J Biol Chem (2021) 297 pp. 101334-101334 [ DOI: doi:10.1016/j.jbc.2021.101334 Pubmed: 34688652 ]
- Full-length ap-3 complex from saccharomyces cerevisiae (Complex from Saccharomyces cerevisiae)
- Ap complex subunit sigma (21 kDa, Protein from Saccharomyces cerevisiae)
- Ap-3 complex subunit mu (54 kDa, Protein from Saccharomyces cerevisiae)
- Ap-3 complex subunit delta (110 kDa, Protein from Saccharomyces cerevisiae)
- Y55_g0035830.mrna.1.cds.1 (91 kDa, Protein from Saccharomyces cerevisiae)