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) [ DOI: doi:10.1038/s41594-024-01257-y Pubmed: 38605244 ]
- 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)
- Unknown (12 kDa, Protein from Homo sapiens)
- Cullin-9 (281 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Nedd8 (9 kDa, Protein from Homo sapiens)
cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 8wqc
Q-score: 0.352
Chen X, Raiff A, Li S, Guo Q, Zhang J, Zhou H, Timms RT, Yao X, Elledge SJ, Koren I, Zhang K, Xu C
Nat Commun (2024) 15 pp. 3558-3558 [ DOI: doi:10.1038/s41467-024-47890-5 Pubmed: 38670995 ]
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (11 kDa, Protein from Homo sapiens)
- Cryo-em structure of neddylated cul2-rbx1-elob-eloc-fem1b bound with the c-degron of cdk5r1 (Complex from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
- Protein fem-1 homolog b (70 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Resolution: 4.09 Å
EM Method: Single-particle
Fitted PDBs: 8wqg
Q-score: 0.265
Chen X, Raiff A, Li S, Guo Q, Zhang J, Zhou H, Timms RT, Yao X, Elledge SJ, Koren I, Zhang K, Xu C
Nat Commun (2024) 15 pp. 3558-3558 [ DOI: doi:10.1038/s41467-024-47890-5 Pubmed: 38670995 ]
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (11 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein fem-1 homolog b (70 kDa, Protein from Homo sapiens)
- Cryo-em structure of neddylated cul2-rbx1-elob-eloc-fem1b bound with the c-degron of ccdc89 (conformation 1) (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 ]
- 5-azanyl-1-oxidanyl-pentan-2-one (117 Da, Ligand)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 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)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Cdc34, nedd8, elob, eloc, fem1c with ube2r2-donor ub-sil1 peptide (Complex from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 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- [ Pubmed: 38382526 DOI: doi:10.1016/j.molcel.2024.01.022 ]
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Von hippel-lindau disease tumor suppressor (18 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 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)
- 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)
- Ubiquitin-conjugating enzyme e2 r2 (25 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (11 kDa, Protein from Homo sapiens)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Bromodomain-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Cdc34, nedd8, elob, eloc, vhl, brd4 with ube2r2-donor ub- brd4 bd2 (Complex 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 ]
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- Elongin-b (13 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)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex 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)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- 5-azanylpentan-2-one (101 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex
Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 8h38
Q-score: 0.078
Hu Y, Zhang Z, Mao Q, Zhang X, Hao A, Xun Y, Wang Y, Han L, Zhan W, Liu Q, Yin Y, Peng C, Moresco EMY, Chen Z, Beutler B, Sun L
Nat Struct Mol Biol (2024) 31 pp. 336-350 [ DOI: doi:10.1038/s41594-023-01182-6 Pubmed: 38332366 ]
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Cop9 signalosome complex subunit 5 (37 kDa, Protein from Homo sapiens)
- Cop9 signalosome complex subunit 6 (36 kDa, Protein from Homo sapiens)
- Cullin-3 (89 kDa, Protein from Homo sapiens)
- Kelch repeat and btb domain-containing protein 2 (71 kDa, Protein from Homo sapiens)
- Cop9 signalosome complex subunit 4 (46 kDa, Protein from Homo sapiens)
- Cop9 signalosome complex subunit 7b (29 kDa, Protein from Homo sapiens)
- Cop9 signalosome complex subunit 1 (59 kDa, Protein from Homo sapiens)
- Cop9 signalosome complex subunit 2 (51 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Nedd8 (Complex)
- Cop9 signalosome complex subunit 3 (47 kDa, Protein from Homo sapiens)
- Kbtbd2-crl3~n8 dimer assemble with csn(mutate) monomer (Complex from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
- Csn (Complex)
- Csn subunit1, kbtbd2, cullin-3, rbx1 (Complex)
- Cop9 signalosome complex subunit 8 (23 kDa, Protein from Homo sapiens)
Cryo-EM Structure of the CAND1-Cul3-Rbx1 complex
Resolution: 3.76 Å
EM Method: Single-particle
Fitted PDBs: 8h3q
Q-score: 0.239
Hu Y, Zhang Z, Mao Q, Zhang X, Hao A, Xun Y, Wang Y, Han L, Zhan W, Liu Q, Yin Y, Peng C, Moresco EMY, Chen Z, Beutler B, Sun L
Nat Struct Mol Biol (2024) 31 pp. 336-350 [ DOI: doi:10.1038/s41594-023-01182-6 Pubmed: 38332366 ]
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Cul3, rbx1 (Complex)
- Cullin-3 (89 kDa, Protein from Homo sapiens)
- Cand1 (Complex)
- Cand1-cul3-rbx1 complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cullin-associated nedd8-dissociated protein 1 (136 kDa, Protein from Homo sapiens)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8b3i
Q-score: 0.466
To Be Published
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- C(n)rl4csa-e2-ub complex. (Complex from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d2 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Cullin-4a (87 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8or0
Q-score: 0.218
Shaaban M, Clapperton JA, Ding S, Kunzelmann S, Maeots ME, Maslen SL, Skehel JM, Enchev RI
Mol Cell (2023) 83 pp. 2332- [ Pubmed: 37339624 DOI: doi:10.1016/j.molcel.2023.05.034 ]
- Cullin-associated nedd8-dissociated protein 1 (137 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinases regulatory subunit 1 (8 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinase 2 (33 kDa, Protein from Homo sapiens)
- Cand1-cul1-rbx1-skp1-skp2-cks1-cdk2 (Complex from Homo sapiens)
- Cullin-1 (93 kDa, Protein from Homo sapiens)
- S-phase kinase-associated protein 2 (48 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- S-phase kinase-associated protein 1 (18 kDa, Protein from Homo sapiens)