Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex
Resolution: 8.4 Å
EM Method: Single-particle
Fitted PDBs: 7okq
Q-score: 0.124
Mohamed WI, Schenk AD, Kempf G, Cavadini S, Basters A, Potenza A, Abdul Rahman W, Rabl J, Reichermeier K, Thoma NH
EMBO J (2021) 40 pp. e108008-e108008 [ Pubmed: 34595758 DOI: doi:10.15252/embj.2021108008 ]
- Cullin-4a (86 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Crl4(dcaf1) (Complex from Homo sapiens)
- Ddb1- and cul4-associated factor 1 (171 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6r8y
Q-score: 0.313
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Dna damage-binding protein 2 (48 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a 6-4pp containing nucleosome (199 kDa, Complex)
- Histones (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with a 6-4pp at positions 95-96 (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Dna damage-binding proteins (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
Cryo-EM structure of NCP_THF2(-1)-UV-DDB
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6r8z
Q-score: 0.307
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Dna damage-binding protein 2 (48 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Uv-ddb bound to a thf2 containing nucleosome (199 kDa, Complex)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6r90
Q-score: 0.278
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Uv-ddb bound to a thf2 containing nucleosome class a (199 kDa, Complex)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 93-94 (44 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of NCP_THF2(-3)-UV-DDB
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6r91
Q-score: 0.212
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a thf2 (-3) containing nucleosome (Complex)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6r92
Q-score: 0.22
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Dna damage-binding protein 1,dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a thf2 (+1) containing nucleosome class b (Complex)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 93-94 (44 kDa, DNA from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of CSN-N8-CRL4A at 6.7 A resolution
Cavadini S, Fischer ES, Bunker RD, Potenza A, Lingaraju GM, Goldie KN, Mohamed WI, Faty M, Petzold G, Beckwith REJ, Tichkule R, Hassiepen U, Abdulrahman W, Pantelic RS, Matsumoto S, Sugasawa K, Stahlberg H, Thoma NH
Nature (2016) 531 pp. 598-603 [ DOI: doi:10.1038/nature17416 Pubmed: 27029275 ]
- Cop9 signalosome subunit 6 (35 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (11 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 1 (52 kDa, Protein from Homo sapiens)
- Cul4a (79 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 5 (35 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 2 (49 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 3 (46 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 7a (30 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 8 (23 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 4 (44 kDa, Protein from Homo sapiens)
- Recombinant human csn-n8-crl4a complex (493 kDa, Sample)
- Dna damage-binding protein 1 (125 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
Rigid part of the CSN-N8-CRL4A cryo-EM structure at 6.4 A resolution
Cavadini S, Fischer ES, Bunker RD, Potenza A, Lingaraju GM, Goldie KN, Mohamed WI, Faty M, Petzold G, Beckwith REJ, Tichkule R, Hassiepen U, Abdulrahman W, Pantelic RS, Matsumoto S, Sugasawa K, Stahlberg H, Thoma NH
Nature (2016) 531 pp. 598-603 [ DOI: doi:10.1038/nature17416 Pubmed: 27029275 ]
- Cop9 signalosome subunit 6 (35 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (11 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 1 (52 kDa, Protein from Homo sapiens)
- Cul4a (79 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 5 (35 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 2 (49 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 3 (46 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 7a (30 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 8 (23 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 4 (44 kDa, Protein from Homo sapiens)
- Recombinant human csn-n8-crl4a complex (493 kDa, Sample)
- Dna damage-binding protein 1 (125 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
Cryo-EM structure of CSN-N8-CRL4A at 8.8 A resolution
Cavadini S, Fischer ES, Bunker RD, Potenza A, Lingaraju GM, Goldie KN, Mohamed WI, Faty M, Petzold G, Beckwith REJ, Tichkule R, Hassiepen U, Abdulrahman W, Pantelic RS, Matsumoto S, Sugasawa K, Stahlberg H, Thoma NH
Nature (2016) 531 pp. 598-603 [ DOI: doi:10.1038/nature17416 Pubmed: 27029275 ]
- Cop9 signalosome subunit 6 (35 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (11 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 1 (52 kDa, Protein from Homo sapiens)
- Cul4a (79 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 5 (35 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 2 (49 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 3 (46 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 7a (30 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 8 (23 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 4 (44 kDa, Protein from Homo sapiens)
- Recombinant human csn-n8-crl4a complex (493 kDa, Sample)
- Dna damage-binding protein 1 (125 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
Cryo-EM structure of CSN-N8-CRL4ADDB2 at 8.3 A resolution
Cavadini S, Fischer ES, Bunker RD, Potenza A, Lingaraju GM, Goldie KN, Mohamed WI, Faty M, Petzold G, Beckwith REJ, Tichkule R, Hassiepen U, Abdulrahman W, Pantelic RS, Matsumoto S, Sugasawa K, Stahlberg H, Thoma NH
Nature (2016) 531 pp. 598-603 [ DOI: doi:10.1038/nature17416 Pubmed: 27029275 ]
- Cop9 signalosome subunit 6 (35 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (11 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 1 (52 kDa, Protein from Homo sapiens)
- Cul4a (79 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (39 kDa, Protein from Danio rerio)
- Cop9 signalosome subunit 5 (35 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 2 (49 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 3 (46 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 7a (30 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 8 (23 kDa, Protein from Homo sapiens)
- Cop9 signalosome subunit 4 (44 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (125 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
- Recombinant human csn-n8-crl4addb2 complex. (533 kDa, Sample)