SMTL ID : 8wqg.1

cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1)

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: 3 residues within 4Å: Chain B: C.41, C.44, H.70 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.41, B:C.44, B:H.70 ZN.2: 4 residues within 4Å: Chain B: C.30, C.33, 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: 5 residues within 4Å: Chain B: C.63, H.65, C.82, L.84, D.85 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.63, B:H.65, B:H.65, B:C.82, B:D.85 ZN.4: 5 residues within 4Å: Chain E: C.41, E.43, C.44, C.56, H.70 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.41, E:C.44, E:C.56, E:H.70, E:H.70 ZN.5: 5 residues within 4Å: Chain E: C.30, C.33, C.41, H.68, C.71 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.30, E:C.33, E:H.68, E:C.71 ZN.6: 4 residues within 4Å: Chain E: C.63, H.65, C.82, D.85 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.63, E:H.65, E:C.82, E: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

Elongin-B: AI
E3 ubiquitin-protein ligase RBX1, N-terminally processed: BE
Elongin-C: CH
Cullin-2: DF
NEDD8: GJ
Protein fem-1 homolog B: KL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

I
I

B
F

E
J

C
B

H
H

D
C

F
E

G
N

J
K

K
A

L
G

Elongin-B

E3 ubiquitin-protein ligase RBX1, N-terminally processed

Elongin-C

Cullin-2

NEDD8

Protein fem-1 homolog B

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