SMTL ID : 6ven.1

Yeast COMPASS in complex with a ubiquitinated nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain N: C.297, C.346, C.348, C.353, K.354 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.297, N:C.346, N:C.348, N:K.354

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

SAM.2: 14 residues within 4Å: Chain N: I.225, H.226, W.228, G.268, S.269, S.270, Y.271, R.291, I.293, N.294, H.295, Y.332, L.347, L.357 10 PLIP interactions: 10 interactions with chain N Hydrogen bonds: N:N.227, N:W.228, N:G.268, N:S.270, N:S.270, N:N.294, N:H.295, N:H.295, N:L.347 pi-Stacking: N:H.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Worden, E.J. et al., Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome. Elife (2020)

Release Date

2020-01-15

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
Ubiquitin: K
COMPASS component SWD3: L
COMPASS component SWD1: M
Histone-lysine N-methyltransferase, H3 lysine-4 specific: N
COMPASS component BRE2: O
COMPASS component SDC1: PQ
COMPASS component SPP1: R

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

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Ubiquitin

COMPASS component SWD3

COMPASS component SWD1

Histone-lysine N-methyltransferase, H3 lysine-4 specific

COMPASS component BRE2

COMPASS component SDC1

COMPASS component SPP1

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