SMTL ID : 8sn9.1

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain K: C.41, H.43, C.61, F.63, 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
Polyubiquitin-B: M

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

M
M

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

Polyubiquitin-B

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