SMTL ID : 8q7r.1

Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-mer

Ligands

1 x U9O: 5-azanyl-1-oxidanyl-pentan-2-one(Covalent)

U9O.1: 6 residues within 4Å: Chain C: R.74, G.75 Chain D: C.1 Chain E: N.85, C.93, S.138 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:C.93

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain H: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.42, H:C.45, H:H.80, H:C.83 ZN.3: 4 residues within 4Å: Chain H: C.75, H.77, C.94, D.97 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.75, H:H.77, H:C.94, H:D.97 ZN.4: 4 residues within 4Å: Chain H: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.53, H:C.56, H:C.68, H:H.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting. Mol.Cell (2024)

Release Date

2024-02-21

Peptides

Cullin-2: A
Protein fem-1 homolog C: B
Ubiquitin: C
Nucleotide exchange factor SIL1: D
Ubiquitin-conjugating enzyme E2 R2: E
Elongin-C: F
Elongin-B: G
E3 ubiquitin-protein ligase RBX1: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
U

D
F

E
C

F
D

G
G

H
R

Cullin-2

Protein fem-1 homolog C

Ubiquitin

Nucleotide exchange factor SIL1

Ubiquitin-conjugating enzyme E2 R2

Elongin-C

Elongin-B

E3 ubiquitin-protein ligase RBX1

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