SMTL ID : 5hyn.2 (7 other biounits)

Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-oligomer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.286, C.289, C.294, H.297 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.286, A:C.289, A:C.294, A:H.297 ZN.2: 4 residues within 4Å: Chain A: C.320, C.324, C.452, C.463 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.320, A:C.324, A:C.452, A:C.463 ZN.3: 5 residues within 4Å: Chain A: C.530, C.543, C.549, C.553 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.530, A:C.543, A:C.549, A:C.553 ZN.4: 7 residues within 4Å: Chain A: C.523, H.525, C.530, C.534, C.543 Ligands: ZN.3, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.523, A:H.525, A:C.530, A:C.534 ZN.5: 5 residues within 4Å: Chain A: C.523, C.536, C.543, C.547 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.523, A:C.536, A:C.543, A:C.547 ZN.6: 7 residues within 4Å: Chain A: C.560, C.566, C.580, C.588, C.601 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.566, A:C.580, A:C.588, A:C.601 ZN.7: 7 residues within 4Å: Chain A: C.560, C.571, C.573, C.580, C.585 Ligands: ZN.6, ZN.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.560, A:C.573, A:C.580, A:C.585 ZN.8: 6 residues within 4Å: Chain A: C.560, C.562, C.566, C.571 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.560, A:C.562, A:C.566, A:C.571

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.9: 18 residues within 4Å: Chain A: V.621, A.622, G.623, W.624, M.662, C.663, S.664, F.665, R.685, F.686, A.687, N.688, H.689, Y.726, A.733, L.734, K.735, Y.736 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.624, A:W.624, A:M.662, A:S.664, A:S.664, A:N.688, A:H.689, A:Y.736, A:Y.736

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Justin, N. et al., Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2. Nat Commun (2016)

Release Date

2016-05-11

Peptides

Histone-lysine N-methyltransferase EZH2: A
Polycomb protein EED: B
Polycomb protein SUZ12: C
H3K27M: D
JARID2 K116me3: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

Histone-lysine N-methyltransferase EZH2

Polycomb protein EED

Polycomb protein SUZ12

H3K27M

JARID2 K116me3

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