SMTL ID : 8sn0.1

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain K: C.41, H.43, C.61, C.64 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.41, K:H.43, K:C.61, K:C.64 ZN.2: 4 residues within 4Å: Chain K: C.26, C.29, C.46, C.49 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.26, K:C.29, K:C.46, K:C.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Q. et al., Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell (2024)

Release Date

2024-01-17

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

K
K

L
L

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

E3 ubiquitin-protein ligase RNF168

Ubiquitin-conjugating enzyme E2 D3

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