8R5H: Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2

PDB ID: 8R5HDownload
MMDB ID: 243073
PDB Deposition Date: 2023/11/16
Updated in MMDB: 2025/12
Experimental Method:
electron microscopy
Resolution: 3.44  Å
Source Organism:
Similar Structures:
Biological Unit for 8R5H: octameric; determined by author
Molecular Components in 8R5H
Label Count Molecule
Proteins (8 molecules)
1
Cullin-2
(Gene symbol: CUL2)
Molecule annotation
1
E3 Ubiquitin-protein Ligase Rbx1, N-terminally Processed
(Gene symbol: RBX1)
Molecule annotation
1
Ubiquitin-conjugating Enzyme E2 R2
(Gene symbol: UBE2R2)
Molecule annotation
1
Ubiquitin
(Gene symbol: UBC)
Molecule annotation
1
Elongin-c
(Gene symbol: ELOC)
Molecule annotation
1
Bromodomain-containing Protein 4
(Gene symbol: BRD4)
Molecule annotation
1
Elongin-b
(Gene symbol: ELOB)
Molecule annotation
1
VON Hippel-lindau Disease Tumor Suppressor
(Gene symbol: VHL)
Molecule annotation
Chemicals and Non-standard biopolymers (5 molecules)
1
3
ZINC IONZINC ION
2
1
5-azanylpentan-2-one5-azanylpentan-2-one
3
1
(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(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
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303