SMTL ID : 9isz.1 (2 other biounits)

Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 17 residues within 4Å: Chain A: K.149, G.150, W.151, G.189, I.190, T.191, Y.192, R.217, F.218, N.220, H.221, Y.262, R.285, Q.287, C.288, K.289, C.290 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.151, A:G.189, A:T.191, A:H.221, A:H.221, A:Y.262, A:R.285, A:K.289 Water bridges: A:Y.192 SAM.6: 19 residues within 4Å: Chain B: K.149, G.150, W.151, G.189, I.190, T.191, Y.192, R.217, F.218, F.219, N.220, H.221, Y.262, Q.287, C.288, K.289, C.290, L.299, G.301 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.150, B:W.151, B:G.189, B:T.191, B:Y.192, B:Y.192, B:H.221, B:H.221, B:K.289

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.223, C.288, C.290, C.295, R.296 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.223, A:C.288, A:C.290, A:C.295 ZN.3: 6 residues within 4Å: Chain A: C.71, C.89, C.118, C.122 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.89, A:C.118, A:C.122 ZN.4: 5 residues within 4Å: Chain A: C.79, C.118, C.124, C.128 Ligands: ZN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.79, A:C.118, A:C.124, A:C.128, H2O.1 ZN.5: 5 residues within 4Å: Chain A: C.71, C.73, C.79, C.87 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.73, A:C.79, A:C.87 ZN.7: 5 residues within 4Å: Chain B: C.223, C.288, C.290, C.295, R.296 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.223, B:C.288, B:C.290, B:C.295 ZN.8: 6 residues within 4Å: Chain B: C.71, C.89, C.118, C.122 Ligands: ZN.9, ZN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.71, B:C.89, B:C.118, B:C.122 ZN.9: 5 residues within 4Å: Chain B: C.71, C.73, C.79, C.87 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.71, B:C.73, B:C.79, B:C.87 ZN.10: 5 residues within 4Å: Chain B: C.79, C.118, C.124, C.128 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.79, B:C.118, B:C.124, B:C.128, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, Y. et al., Mechanistic insights into the stimulation of the histone H3K9 methyltransferase Clr4 by proximal H3K14 ubiquitination. Sci Adv (2025)

Release Date

2025-04-30

Peptides

Histone-lysine N-methyltransferase, H3 lysine-9 specific: AB
Ubiquitin: CD
Histone H3.1/H3.2: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Histone-lysine N-methyltransferase, H3 lysine-9 specific

Ubiquitin

Histone H3.1/H3.2

Related Entries With Identical Sequence