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SMTL ID : 6uh5.1

Structural basis of COMPASS eCM recognition of the H2Bub nucleosome

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ALA-ARG-THR-MET-GLN-THR-ALA-ARG.1:

13 residues within 4Å:

Chain L: E.176, S.187, L.189, F.190, R.191, A.220, I.222, Y.247, Y.249, K.250, F.251, E.252
Ligands: SAM.3

17 PLIP interactions:

17 interactions with chain L

Hydrophobic interactions: L:F.190, L:R.191, L:I.222, L:E.252
Hydrogen bonds: L:E.176, L:E.176, L:S.187, L:L.189, L:L.189, L:R.191, L:Y.247, L:Y.249, L:K.250, L:K.250, L:K.250, L:E.252, L:E.252

1 x ZN: ZINC ION(Non-covalent)

ZN.2:

3 residues within 4Å:

Chain L: C.263, C.265, C.270

3 PLIP interactions:

3 interactions with chain L

Metal complexes: L:C.263, L:C.265, L:C.270

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

SAM.3:

18 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, C.263, L.264, C.265, L.274
Ligands: ALA-ARG-THR-MET-GLN-THR-ALA-ARG.1

11 PLIP interactions:

11 interactions with chain L

Hydrophobic interactions: L:Y.188
Hydrogen bonds: L:W.145, L:W.145, L:W.145, L:S.186, L:S.186, L:Y.188, L:Y.249, L:L.264, L:C.265
Salt bridges: L:H.143

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: H
Swd3: K
Histone-lysine N-methyltransferase, H3 lysine-4 specific: L
Swd1: M
Ubiquitin: N
Spp1: O
Bre2: P
Sdc1: QR

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
Q

O
X

P
L

Q
O

R
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

Swd3

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

Swd1

Ubiquitin

Spp1

Bre2

Sdc1

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