SMTL ID : 7ea5.1

Yeast Set2 bound to a nucleosome containing oncohistone mutations

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain K: C.50, C.65, C.73, C.77 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.50, K:C.65, K:C.73 ZN.2: 5 residues within 4Å: Chain K: C.36, C.38, C.50, C.56 Ligands: ZN.1 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.36, K:C.38, K:C.50 ZN.3: 4 residues within 4Å: Chain K: C.169, C.216, C.218, C.223 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:C.216, K:C.223

1 x SAM: S-ADENOSYLMETHIONINE(Covalent)

SAM.4: 16 residues within 4Å: Chain K: K.98, G.99, Y.100, H.141, F.142, Y.143, R.163, F.164, C.165, N.166, H.167, Y.204, Q.214, K.215, C.216, Y.217 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:Y.100, K:Y.100, K:F.142, K:F.142, K:H.167, K:H.167, K:Q.214, K:Y.217 Salt bridges: K:H.141 pi-Cation interactions: K:H.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations. Cell Discov (2021)

Release Date

2021-07-14

Peptides

Histone H3: AE
Histone H4: BF
Histone H2A: CG
Histone H2B: DH
Histone-lysine N-methyltransferase, H3 lysine-36 specific: K

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

Histone H3

Histone H4

Histone H2A

Histone H2B

Histone-lysine N-methyltransferase, H3 lysine-36 specific

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