SMTL ID : 8pql.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SY8.1: 8 residues within 4Å: Chain A: N.85, C.93, S.138, P.139, A.140 Chain B: A.46, C.48 Chain E: G.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85, A:C.93

3 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liwocha, J. et al., Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-02-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
H

D
K

E
U

F
A

G
D

H
G

Ubiquitin-conjugating enzyme E2 R2

Polyubiquitin-C,Nucleotide exchange factor SIL1

Protein fem-1 homolog C

E3 ubiquitin-protein ligase RBX1

Ubiquitin

Cullin-2

Elongin-C

Elongin-B

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