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SMTL ID : 6ugm.1

Structural basis of COMPASS eCM recognition of an unmodified nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x THR- MET- GLN: H3 N-terminus(Non-covalent)

THR-MET-GLN.1:

9 residues within 4Å:

Chain L: S.187, L.189, F.190, R.191, Y.247, Y.249, K.250, F.251
Ligands: SAM.2

4 PLIP interactions:

4 interactions with chain L

Hydrophobic interactions: L:L.189, L:F.190
Hydrogen bonds: L:R.191, L:Y.247

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

SAM.2:

19 residues within 4Å:

Chain L: I.142, H.143, W.145, G.185, S.186, S.187, Y.188, R.208, F.209, I.210, N.211, H.212, Y.249, P.262, C.263, L.264, C.265, L.274
Ligands: THR-MET-GLN.1

6 PLIP interactions:

6 interactions with chain L

Hydrophobic interactions: L:Y.188
Hydrogen bonds: L:H.143, L:S.186, L:N.211, L:L.264
Salt bridges: L:R.208

1 x ZN: ZINC ION(Non-covalent)

ZN.3:

5 residues within 4Å:

Chain L: E.215, C.263, C.265, A.267, C.270

1 PLIP interactions:

1 interactions with chain L

Metal complexes: L:C.263

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Hsu, P.L. et al., Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS. Mol.Cell (2019)

Release Date

2019-11-20

Peptides

Histone H3: AE
Histone H4: BF
Histone H2A: CG
Histone H2B: D
Histone H2B 1.1: H
Swd3: K
Histone-lysine N-methyltransferase, H3 lysine-4 specific: L
Swd1: M
Spp1: N
Bre2: O
Sdc1: PQ

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
M

M
N

N
X

O
L

P
O

Q
P

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3

Histone H4

Histone H2A

Toggle Identical (CG)

Histone H2B

Histone H2B 1.1

Swd3

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

Swd1

Spp1

Bre2

Sdc1

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