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. 1304-1320.e16 [ DOI: doi:10.1016/j.molcel.2024.01.022 Pubmed: 38382526 ]
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)
EGFR:Degrader:VHL:Elongin-B/C:Cul2
Rosenberg SC, Shanahan F, Yamazoe S, Kschonsak M, Zeng YJ, Lee J, Plise E, Yen I, Rose CM, Quinn JG, Gazzard LJ, Walters BT, Kirkpatrick DS, Staben ST, Foster SA, Malek S
Cell Chem Biol (2023) [ Pubmed: 36773603 DOI: doi:10.1016/j.chembiol.2023.01.007 ]
Ribosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation
Resolution: 9.6 Å
EM Method: Single-particle
Fitted PDBs: 3bo0, 3bo1
Q-score: 0.0755
Menetret JF, Schaletzky J, Clemons WM Jr, Osborne AR, Skanland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW
Mol Cell (2007) 28 pp. 1083-1092 [ Pubmed: 18158904 DOI: doi:10.1016/j.molcel.2007.10.034 ]
- Ribosome secy complex (3 MDa, Sample)
- 70s ribosome (3 MDa, Complex from Escherichia coli)