SMTL ID : 8x7k.1

Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-2-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain L: C.31, H.33, C.51, C.54, R.56 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:H.33, L:C.51, L:C.54 ZN.2: 4 residues within 4Å: Chain L: C.16, C.19, C.36, C.39 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.16, L:C.19, L:C.36, L:C.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ai, H. et al., Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168. Biorxiv (2024)

Release Date

2024-08-07

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1-B/E: C
Histone H2B type 1-K: DH
Histone H2A type 1-B/E: G
Ubiquitin-conjugating enzyme E2 D3: K
E3 ubiquitin-protein ligase RNF168: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

D
D

H
H

G
G

K
K

L
L

Histone H3.2

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-K

Histone H2A type 1-B/E

Ubiquitin-conjugating enzyme E2 D3

E3 ubiquitin-protein ligase RNF168

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