SMTL ID : 8grm.1

Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain I: C.17, C.20, C.38, C.41 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.38, I:C.41 ZN.2: 4 residues within 4Å: Chain I: C.33, H.35, C.52, C.55 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.33, I:H.35, I:C.52, I:C.55 ZN.3: 4 residues within 4Å: Chain J: C.36, C.39, C.57, C.60 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.36, J:C.39, J:C.57, J:C.60 ZN.4: 4 residues within 4Å: Chain J: C.52, H.54, C.72, C.75 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.52, J:H.54, J:C.72, J:C.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ai, H.S. et al., Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination. Chem (2023)

Release Date

2023-04-12

Peptides

Histone H3: AE
Histone H4: BF
Histone H2A type 1-B/E: CG
Histone H2B type 1-K: D
Histone H2B type 1-K: H
COMMD3 protein: I
Ring1B: J
Ubiquitin: M
UbcH5b: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

I
M

J
N

M
O

N
P

Histone H3

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-K

Histone H2B type 1-K

COMMD3 protein

Ring1B

Ubiquitin

UbcH5b

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