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)
nsEM map of E1E2 AMS0232 glycoprotein in complex with monoclonal antibody AR4A
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 ]
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 bound to CC-92480, Focused Refinement
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 (Protein from Homo sapiens)
- Cereblon bound to cc-92480 (Complex 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)