Scalable protein design using hallucination in a relaxed sequence space
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 9exk
Q-score: 0.422
Frank C, Khoshouei A, Fu beta L, Schiwietz D, Putz D, Weber L, Zhao Z, Hattori M, Feng S, de Stigter Y, Ovchinnikov S, Dietz H
Science (2024) 386 pp. 439-445 [ Pubmed: 39446959 DOI: doi:10.1126/science.adq1741 ]
- De novo designed protein k12 (114 kDa, Cellular component from synthetic construct)
- De novo designed protein k12 (115 kDa, Protein from synthetic construct)
Scalable protein design using hallucination in a relaxed sequence space
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 9f0l
Q-score: 0.52
Frank C, Khoshouei A, Fu beta L, Schiwietz D, Putz D, Weber L, Zhao Z, Hattori M, Feng S, de Stigter Y, Ovchinnikov S, Dietz H
Science (2024) 386 pp. 439-445 [ Pubmed: 39446959 DOI: doi:10.1126/science.adq1741 ]
- De novo designed protein k10 (106 kDa, Protein from synthetic construct)
- De novo designed protein k10 (106 kDa, Cellular component from synthetic construct)
Resolution: 4.16 Å
EM Method: Single-particle
Fitted PDBs: 9bei
Q-score: 0.276
Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE
Nature (2024) 631 pp. 449-458 [ Pubmed: 38898281 DOI: doi:10.1038/s41586-024-07601-y ]
- Cop-2 fab heavy chain (25 kDa, Protein from Escherichia coli)
- Anti-fab nanobody (13 kDa, Protein from Escherichia coli)
- Claudin-4 (22 kDa, Protein from Homo sapiens)
- Synthetic human claudin-4 complex with clostridium perfringens enterotoxin c-terminal domain, sfab cop-2, and nanobody against cop-2 (103 kDa, Complex from Homo sapiens)
- Heat-labile enterotoxin b chain (14 kDa, Protein from Clostridium perfringens)
- Cop-2 fab light chain (23 kDa, Protein from Escherichia coli)
Uncharacterized Q8U0N8 protein from Pyrococcus furiosus
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8p49
Q-score: 0.504
Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED
Cell (2024) 187 pp. 999- [ DOI: doi:10.1016/j.cell.2024.01.022 Pubmed: 38325366 ]
Cysteine tRNA ligase homodimer
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8qhp
Q-score: 0.546
Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED
Cell (2024) 187 pp. 999- [ DOI: doi:10.1016/j.cell.2024.01.022 Pubmed: 38325366 ]
- Cysteine--trna ligase (57 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Homodimeric form of cysteine trna ligase (114 kDa, Complex from Pyrococcus furiosus DSM 3638)
Cryo-EM structure of designed Influenza HA binder, HA_20, bound to Influenza HA (Strain: Iowa43)
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8sk7
Q-score: 0.528
Watson JL, Juergens D, Bennett NR, Trippe BL, Yim J, Eisenach HE, Ahern W, Borst AJ, Ragotte RJ, Milles LF, Wicky BIM, Hanikel N, Pellock SJ, Courbet A, Sheffler W, Wang J, Venkatesh P, Sappington I, Torres SV, Lauko A, De Bortoli V, Mathieu E, Ovchinnikov S, Barzilay R, Jaakkola TS, DiMaio F, Baek M, Baker D
Nature (2023) 620 pp. 1089-1100 [ DOI: doi:10.1038/s41586-023-06415-8 Pubmed: 37433327 ]
- Hemagglutinin ha1 chain (35 kDa, Protein from Influenza A virus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hemagglutinin (26 kDa, Protein from Influenza A virus)
- Influenza ha (iowa43) bound to rfdiffusion designed minibinder, ha_20 (Complex from Influenza A virus)
- Ha_20 minibinder (rfdiffusion-designed) (7 kDa, Protein from synthetic construct)
Single particle Data of the activated B. subtilis ClpC arranged as a tetramer of hexamers
Morreale FE, Kleine S, Leodolter J, Junker S, Hoi DM, Ovchinnikov S, Okun A, Kley J, Kurzbauer R, Junk L, Guha S, Podlesainski D, Kazmaier U, Boehmelt G, Weinstabl H, Rumpel K, Schmiedel VM, Hartl M, Haselbach D, Meinhart A, Kaiser M, Clausen T
Cell (2022) 185 pp. 2203-2205 [ DOI: 10.1016/j.cell.2022.05.009 Pubmed: 35662409 ]
Image sets:
Cryo-EM structure of B. subtilis ClpC (DWB mutant) hexamer bound to a substrate polypeptide
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7abr
Q-score: 0.454
Morreale FE, Kleine S, Leodolter J, Junker S, Hoi DM, Ovchinnikov S, Okun A, Kley J, Kurzbauer R, Junk L, Guha S, Podlesainski D, Kazmaier U, Boehmelt G, Weinstabl H, Rumpel K, Schmiedel VM, Hartl M, Haselbach D, Meinhart A, Kaiser M, Clausen T
Cell (2022) 185 pp. 2338- [ DOI: doi:10.1016/j.cell.2022.05.009 Pubmed: 35662409 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- B. subtilis clpc (dwb mutant) hexamer bound to a substrate polypeptide (Complex from Bacillus subtilis subsp. subtilis str. 168)
- Substrate polypeptide (Complex from unidentified)
- Substrate polypeptide (2 kDa, Protein from unidentified)
- Negative regulator of genetic competence clpc/mecb (Complex from Bacillus subtilis subsp. subtilis str. 168)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Negative regulator of genetic competence clpc/mecb (91 kDa, Protein from Bacillus subtilis (strain 168))
Cryo-EM map of the activated B. subtilis ClpC arranged as a tetramer of hexamers
Morreale FE, Kleine S, Leodolter J, Junker S, Hoi DM, Ovchinnikov S, Okun A, Kley J, Kurzbauer R, Junk L, Guha S, Podlesainski D, Kazmaier U, Boehmelt G, Weinstabl H, Rumpel K, Schmiedel VM, Hartl M, Haselbach D, Meinhart A, Kaiser M, Clausen T
Cell (2022) 185 pp. 2338-2353.e18 [ DOI: doi:10.1016/j.cell.2022.05.009 Pubmed: 35662409 ]
Cryo-EM map of Hrd1/Hrd3 monomer
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6vjy
Q-score: 0.334
Wu X, Siggel M, Ovchinnikov S, Mi W, Svetlov V, Nudler E, Liao M, Hummer G, Rapoport TA
Science (2020) 368 [ Pubmed: 32327568 DOI: doi:10.1126/science.aaz2449 ]