SMTL ID : 7b5n.1

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.344, C.347, C.362, C.367 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.344, B:C.347, B:C.362, B:C.367 ZN.2: 4 residues within 4Å: Chain B: C.372, C.375, H.382, C.389 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.372, B:C.375, B:H.382, B:C.389 ZN.3: 4 residues within 4Å: Chain B: C.276, C.281, C.297, C.299 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.276, B:C.281, B:C.297, B:C.299 ZN.4: 4 residues within 4Å: Chain B: C.304, C.307, H.312, C.317 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.304, B:C.307, B:H.312, B:C.317 ZN.5: 5 residues within 4Å: Chain B: C.186, I.188, C.189, C.208, C.211 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.186, B:C.189, B:C.208, B:C.211 ZN.6: 4 residues within 4Å: Chain B: C.203, H.205, C.231, C.236 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.203, B:H.205, B:C.231, B:C.236 ZN.8: 4 residues within 4Å: Chain E: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.42, E:C.45, E:H.80, E:C.83 ZN.9: 4 residues within 4Å: Chain E: C.75, H.77, C.94, D.97 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.75, E:H.77, E:C.94, E:D.97, E:D.97 ZN.10: 4 residues within 4Å: Chain E: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.53, E:C.56, E:C.68, E:H.82

1 x SY8: 5-azanylpentan-2-one(Covalent)

SY8.7: 4 residues within 4Å: Chain B: C.357 Chain C: R.74, G.75 Chain F: C.86 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horn-Ghetko, D. et al., Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly. Nature (2021)

Release Date

2021-02-10

Peptides

Cullin-1: A
E3 ubiquitin-protein ligase ARIH1: B
Polyubiquitin-C: C
NEDD8: D
E3 ubiquitin-protein ligase RBX1: E
Ubiquitin-conjugating enzyme E2 L3: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
U

D
N

E
R

F
D

Cullin-1

E3 ubiquitin-protein ligase ARIH1

Polyubiquitin-C

NEDD8

E3 ubiquitin-protein ligase RBX1

Ubiquitin-conjugating enzyme E2 L3

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