Structure of the non-canonical CTLH E3 substrate receptor WDR26 bound to YPEL5
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8qbn
Q-score: 0.581
Gottemukkala KV, Chrustowicz J, Sherpa D, Sepic S, Vu DT, Karayel O, Papadopoulou EC, Gross A, Schorpp K, von Gronau S, Hadian K, Murray PJ, Mann M, Schulman BA, Alpi AF
Mol Cell (2024) 84 pp. 1948-1963.e11 [ Pubmed: 38759627 DOI: doi:10.1016/j.molcel.2024.04.014 ]
- Protein yippee-like 5 (13 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 26 (70 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Complex of human wdr26-ctlh e3 ligase bound to ypel5 (900 kDa, Complex from Homo sapiens)
Structure of the non-canonical CTLH E3 substrate receptor WDR26 bound to NMNAT1 substrate
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qe8
Q-score: 0.53
Gottemukkala KV, Chrustowicz J, Sherpa D, Sepic S, Vu DT, Karayel O, Papadopoulou EC, Gross A, Schorpp K, von Gronau S, Hadian K, Murray PJ, Mann M, Schulman BA, Alpi AF
Mol Cell (2024) 84 pp. 1948-1963.e11 [ Pubmed: 38759627 DOI: doi:10.1016/j.molcel.2024.04.014 ]
- Zinc ion (65 Da, Ligand)
- Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 (31 kDa, Protein from Homo sapiens)
- Beta-nicotinamide ribose monophosphate (335 Da, Ligand)
- Complex of human wdr26-ctlh e3 ligase bound to nmnat1 (1 MDa, Complex from Homo sapiens)
- Wd repeat-containing protein 26 (70 kDa, Protein from Homo sapiens)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8q7h
Q-score: 0.39
Horn-Ghetko D, Hopf LVM, Tripathi-Giesgen I, Du J, Kostrhon S, Vu DT, Beier V, Steigenberger B, Prabu JR, Stier L, Bruss EM, Mann M, Xiong Y, Schulman BA
Nat Struct Mol Biol (2024) 31 pp. 1083-1094 [ Pubmed: 38605244 DOI: doi:10.1038/s41594-024-01257-y ]
- Zinc ion (65 Da, Ligand)
- Cullin-9 (281 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Structure of cul9-rbx1 ubiquitin e3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer (Complex from Homo sapiens)
- Nedd8 (9 kDa, Protein from Homo sapiens)
- Unknown (12 kDa, Protein from Homo sapiens)
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8rhz
Q-score: 0.425
Horn-Ghetko D, Hopf LVM, Tripathi-Giesgen I, Du J, Kostrhon S, Vu DT, Beier V, Steigenberger B, Prabu JR, Stier L, Bruss EM, Mann M, Xiong Y, Schulman BA
Nat Struct Mol Biol (2024) 31 pp. 1083-1094 [ Pubmed: 38605244 DOI: doi:10.1038/s41594-024-01257-y ]
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cullin-9 (281 kDa, Protein from Homo sapiens)
- Structure of cul9-rbx1 ubiquitin e3 ligase complex in unneddylated conformation - symmetry expanded unneddylated dimer (Complex from Homo sapiens)
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 ]
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cdc34, nedd8, elob, eloc, fem1c with ube2r2-donor ub-sil1 peptide (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- Nucleotide exchange factor sil1 (2 kDa, Protein from Homo sapiens)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- 5-azanyl-1-oxidanyl-pentan-2-one (117 Da, Ligand)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- 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)
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 ]
- Zinc ion (65 Da, Ligand)
- (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)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Bromodomain-containing protein 4 (13 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (11 kDa, Protein from Homo sapiens)
- Cdc34, nedd8, elob, eloc, vhl, brd4 with ube2r2-donor ub- brd4 bd2 (Complex from Homo sapiens)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (25 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- 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)
- Von hippel-lindau disease tumor suppressor (18 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- 5-azanylpentan-2-one (101 Da, Ligand)
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 ]
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase rbx1 (12 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)
- Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- 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)
- 5-azanylpentan-2-one (101 Da, Ligand)
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 ]
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Complex of human ctlhsr4 e3 ligase bound to engineered armc8-specific vh and multiphosphorylated ube2h~ubiquitin (600 kDa, Complex from Homo sapiens)
- E3 ubiquitin-protein transferase rmnd5a (44 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 h (21 kDa, Protein from Homo sapiens)
- 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 ]
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2-24 kda (24 kDa, Protein from Saccharomyces cerevisiae)
- E3 ubiquitin-protein ligase rmd5 (49 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)
- Protein fyv10 (59 kDa, Protein from Saccharomyces cerevisiae)
Structure of the UBE1L activating enzyme bound to ISG15 and UBE2L6
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8oif
Q-score: 0.513
Wallace I, Baek K, Prabu JR, Vollrath R, von Gronau S, Schulman BA, Swatek KN
Nat Commun (2023) 14 pp. 7970-7970 [ Pubmed: 38042859 DOI: doi:10.1038/s41467-023-43711-3 ]
- Ternary complex consisting of ube1l, ube2l6, and full-length isg15. (Complex from Homo sapiens)
- Ubiquitin-like protein isg15 (17 kDa, Protein from Homo sapiens)
- Ubiquitin-like modifier-activating enzyme 7 (111 kDa, Protein from Homo sapiens)
- Ube2l6 (Complex from Homo sapiens)
- Ubiquitin/isg15-conjugating enzyme e2 l6 (17 kDa, Protein from Homo sapiens)
- Adenosine monophosphate (347 Da, Ligand)
- Isg15 (Complex from Homo sapiens)