SMTL ID : 8pp7.1

human RYBP-PRC1 bound to mononucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.18, C.21, C.39, C.42 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.18, A:C.21, A:C.39, A:C.42 ZN.2: 4 residues within 4Å: Chain A: C.34, H.36, C.53, C.56 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.34, A:H.36, A:C.53, A:C.56 ZN.3: 4 residues within 4Å: Chain B: C.55, C.58, C.76, C.79 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.55, B:C.58, B:C.76, B:C.79 ZN.4: 4 residues within 4Å: Chain B: C.71, H.73, C.91, C.94 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.71, B:H.73, B:C.91, B:C.94 ZN.5: 4 residues within 4Å: Chain C: C.18, C.21, C.39, C.42 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.18, C:C.21, C:C.39, C:C.42 ZN.6: 4 residues within 4Å: Chain C: C.34, H.36, C.53, C.56 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.34, C:H.36, C:C.53, C:C.56 ZN.7: 4 residues within 4Å: Chain D: C.55, C.58, C.76, C.79 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.55, D:C.58, D:C.76, D:C.79 ZN.8: 5 residues within 4Å: Chain D: C.71, H.73, C.91, T.93, C.94 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.71, D:H.73, D:C.91, D:C.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciapponi, M. et al., Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-03-27

Peptides

Polycomb complex protein BMI-1: AC
E3 ubiquitin-protein ligase RING2: BD
Histone H3 (Fragment): EI
Histone H4: FJ
Histone H2A: GK
Histone H2B: HL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

C
M

B
L

D
N

E
A

I
E

F
B

J
F

G
C

K
G

H
D

L
H

Polycomb complex protein BMI-1

E3 ubiquitin-protein ligase RING2

Histone H3 (Fragment)

Histone H4

Histone H2A

Histone H2B

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