SMTL ID : 8wqh.1

cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.41, C.44, C.56, H.70 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.41, B:C.44, B:C.56, B:H.70 ZN.2: 5 residues within 4Å: Chain B: C.30, C.33, C.41, H.68, C.71 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.30, B:C.33, B:H.68, B:C.71 ZN.3: 4 residues within 4Å: Chain B: C.63, H.65, C.82, D.85 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.63, B:H.65, B:C.82 ZN.4: 4 residues within 4Å: Chain D: C.41, C.44, C.56, H.70 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.41, D:C.44, D:C.56, D:H.70 ZN.5: 6 residues within 4Å: Chain D: C.30, C.33, N.35, C.41, H.68, C.71 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.30, D:C.33, D:H.68, D:C.71 ZN.6: 4 residues within 4Å: Chain D: C.63, H.65, C.82, D.85 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.63, D:H.65, D:C.82, D:D.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Mechanism of Psi-Pro/C-degron recognition by the CRL2 FEM1B ubiquitin ligase. Nat Commun (2024)

Release Date

2024-04-03

Peptides

Cullin-2: AC
E3 ubiquitin-protein ligase RBX1, N-terminally processed: BD
Elongin-C: EH
Elongin-B: FI
Protein fem-1 homolog B: GK
Coiled-coil domain-containing protein 89: JL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

B
J

D
B

E
E

H
I

F
F

I
K

G
D

K
H

J
G

L
L

Cullin-2

E3 ubiquitin-protein ligase RBX1, N-terminally processed

Elongin-C

Elongin-B

Protein fem-1 homolog B

Coiled-coil domain-containing protein 89

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