SMTL ID : 6nj9.1

Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SAM.1: 21 residues within 4Å: Chain E: L.79 Chain K: P.133, E.134, V.135, G.137, E.138, T.139, D.161, G.163, S.164, G.165, Q.168, V.169, E.186, K.187, A.188, D.222, F.223, L.224, N.241, F.245 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:T.139, K:G.163, K:Q.168, K:Q.168, K:K.187, K:A.188, K:D.222, K:F.223, K:N.241 pi-Stacking: K:F.223 SAM.2: 21 residues within 4Å: Chain A: L.79 Chain M: P.133, E.134, V.135, G.137, E.138, T.139, D.161, G.163, S.164, G.165, Q.168, V.169, E.186, K.187, A.188, D.222, F.223, L.224, N.241, F.245 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:T.139, M:G.163, M:Q.168, M:Q.168, M:K.187, M:A.188, M:D.222, M:F.223, M:N.241 pi-Stacking: M:F.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Worden, E.J. et al., Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L. Cell (2019)

Release Date

2019-02-20

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
Histone-lysine N-methyltransferase, H3 lysine-79 specific: KM
Ubiquitin: LN

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

M
M

L
L

N
N

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Histone-lysine N-methyltransferase, H3 lysine-79 specific

Ubiquitin

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