Resolution: 3.83 Å
EM Method: Single-particle
Fitted PDBs: 7t6x
Q-score: 0.381
Torrents de la Pena A, Sliepen K, Eshun-Wilson L, Newby ML, Allen JD, Zon I, Koekkoek S, Chumbe A, Crispin M, Schinkel J, Lander GC, Sanders RW, Ward AB
Science (2022) 378 pp. 263-269 [ DOI: doi:10.1126/science.abn9884 Pubmed: 36264808 ]
- Igh505, lambda light chain (24 kDa, Protein from Homo sapiens)
- At12009 crossmab, light kappa chain (24 kDa, Protein from Homo sapiens)
- Ar4a fab, heavy chain (29 kDa, Protein from Homo sapiens)
- Ar4a, kappa light chain (25 kDa, Protein from Homo sapiens)
- Envelope glycoprotein e2 (40 kDa, Protein from Hepacivirus C)
- Igh505, heavy chain (52 kDa, Protein from Homo sapiens)
- Envelope glycoprotein e1 (20 kDa, Protein from Hepacivirus C)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- At12009 crossmab, heavy chain (29 kDa, Protein from Homo sapiens)
- Cryoem structure of full-length hepatitis c virus e1e2 glycoprotein in complex with ar4a, at12009 and igh505 fabs (Complex from Hepacivirus C)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8cvp
Q-score: 0.465
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Cereblon~ddb1 in the apo form (177 kDa, Complex from Homo sapiens)
Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8d7u
Q-score: 0.515
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Mezigdomide (567 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Cereblon~ddb1 bound to cc-92480 with ddb1 in the linear conformation (177 kDa, Complex from Homo sapiens)
Cereblon~DDB1 bound to CC-92480 with DDB1 in the twisted conformation
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8d7v
Q-score: 0.45
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Mezigdomide (567 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Cereblon~ddb1 bound to cc-92480 with ddb1 in the twisted conformation (177 kDa, Complex from Homo sapiens)
Cereblon~DDB1 bound to CC-92480 with DDB1 in the hinged conformation
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8d7w
Q-score: 0.476
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Cereblon~ddb1 bound to cc-92480 with ddb1 in the hinged conformation (177 kDa, Complex from Homo sapiens)
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Mezigdomide (567 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
Cereblon~DDB1 in the Apo form with DDB1 in the hinged conformation
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8d7x
Q-score: 0.488
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Zinc ion (65 Da, Ligand)
- Cereblon~ddb1 in the apo form with ddb1 in the hinged conformation (177 kDa, Complex from Homo sapiens)
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
Cereblon-DDB1 in the Apo form with DDB1 in the twisted conformation
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8d7y
Q-score: 0.453
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Zinc ion (65 Da, Ligand)
- Cereblon~ddb1 in the apo form with ddb1 in twisted conformation (177 kDa, Complex from Homo sapiens)
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8d7z
Q-score: 0.492
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Cereblon-ddb1 bound to cc-92480 and ikaros (177 kDa, Complex from Homo sapiens)
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Dna-binding protein ikaros (9 kDa, Protein from Homo sapiens)
- Mezigdomide (567 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8d80
Q-score: 0.457
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Dna-binding protein ikaros (9 kDa, Protein from Homo sapiens)
- Cereblon~ddb1 bound to iberdomide and ikaros zf1-2-3 (177 kDa, Complex from Homo sapiens)
- (3s)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2h-isoindol-2-yl]piperidine-2,6-dione (449 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
Cereblon~DDB1 bound to Pomalidomide
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8d81
Q-score: 0.436
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Cereblon~ddb1 bound to pomalidomide (143 kDa, Complex from Homo sapiens)
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- S-pomalidomide (273 Da, Ligand)
- Dna damage-binding protein 1 (93 kDa, Protein from Homo sapiens)