Resolution: 3.71 Å
EM Method: Single-particle
Fitted PDBs: 8q7r
Q-score: 0.324
Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G
Mol Cell (2024) 84 pp. 1304- [ DOI: doi:10.1016/j.molcel.2024.01.022 Pubmed: 38382526 ]
- Ubiquitin ligation to substrate by a cullin-ring e3 ligase & cdc34: nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2~donor ub-sil1 peptide (180 kDa, Complex)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- Cdc34, nedd8, elob, eloc, fem1c with ube2r2-donor ub-sil1 peptide (Complex from Homo sapiens)
- 5-azanyl-1-oxidanyl-pentan-2-one (117 Da, Ligand)
- Nucleotide exchange factor sil1 (2 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8r5h
Q-score: 0.394
Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G
Mol Cell (2024) 84 pp. 1304- [ DOI: doi:10.1016/j.molcel.2024.01.022 Pubmed: 38382526 ]
- Ubiquitin ligation to neosubstrate by a cullin-ring e3 ligase and cdc34: nedd8-cul2-rbx1-elob/c-vhl-mz1 with trapped ube2r2~donor ub-brd4 bd2 (190 kDa, Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Von hippel-lindau disease tumor suppressor (18 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Bromodomain-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (25 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- 5-azanylpentan-2-one (101 Da, Ligand)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (11 kDa, Protein from Homo sapiens)
- (2~{s},4~{r})-1-[(2~{s})-2-[2-[2-[2-[2-[2-[(9~{s})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{n}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide (1 kDa, Ligand)
- Cdc34, nedd8, elob, eloc, vhl, brd4 with ube2r2-donor ub- brd4 bd2 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
Resolution: 3.76 Å
EM Method: Single-particle
Fitted PDBs: 8pql
Q-score: 0.431
Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G
Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]
- Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Cdc34, nedd8, elob, eloc, fem1c with ube2r2-donor ub-acceptor ub-sil1 peptide and k48-linked ubiquitin chain (Complex from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- 5-azanylpentan-2-one (101 Da, Ligand)
- K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
Catalytic module of human CTLH E3 ligase bound to multiphosphorylated UBE2H~ubiquitin
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8pjn
Q-score: 0.529
Chrustowicz J, Sherpa D, Li J, Langlois CR, Papadopoulou EC, Vu DT, Hehl LA, Karayel O, Beier V, von Gronau S, Muller J, Prabu JR, Mann M, Kleiger G, Alpi AF, Schulman BA
Mol Cell (2024) 84 pp. 293- [ DOI: doi:10.1016/j.molcel.2023.11.027 Pubmed: 38113892 ]
- Complex of human ctlhsr4 e3 ligase bound to engineered armc8-specific vh and multiphosphorylated ube2h~ubiquitin (600 kDa, Complex from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 h (21 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein transferase rmnd5a (44 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein transferase maea (45 kDa, Protein from Homo sapiens)
Catalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin
Resolution: 3.53 Å
EM Method: Single-particle
Fitted PDBs: 8pmq
Q-score: 0.514
Chrustowicz J, Sherpa D, Li J, Langlois CR, Papadopoulou EC, Vu DT, Hehl LA, Karayel O, Beier V, von Gronau S, Muller J, Prabu JR, Mann M, Kleiger G, Alpi AF, Schulman BA
Mol Cell (2024) 84 pp. 293- [ DOI: doi:10.1016/j.molcel.2023.11.027 Pubmed: 38113892 ]
- Protein fyv10 (59 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2-24 kda (24 kDa, Protein from Saccharomyces cerevisiae)
- Complex of yeast chelator-gidsr4 e3 ligase, tetrameric fbp1 substrate and multiphosphorylated ubc8~ubiquitin (1 MDa, Complex from Saccharomyces cerevisiae)
- E3 ubiquitin-protein ligase rmd5 (49 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)