4MI5: EZH2 SET domain

Crystal structure of the EZH2 SET domain. Determined by X-ray diffraction at 2.0 Å resolution. Released 8 Jan 2014.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,775
Mol. weight: 26.46 kDa
Ligands: ZN
Released: 8 Jan 2014

Explore 4MI5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MI5 contains 9 α-helices and 18 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	526-528	3
α-helix	540-543	4
β-strand	548	1	1
β-strand	561	1	1
β-strand	570	1	2
α-helix	577-580	4
β-strand	583	1	3
β-strand	606	1	2
α-helix	610-613	4
β-strand	619-623	5	4
β-strand	629-633	5	4
β-strand	637	1	5
β-strand	642-645	4	3
β-strand	649-652	4	6
α-helix	653-661	9
β-strand	671-673	3	6
β-strand	678-681	4	6
α-helix	688-691	4
α-helix	692	1
β-strand	693-694	2	7
β-strand	700-707	8	3
β-strand	710-717	8	3
β-strand	721	1	5
α-helix	725	1
β-strand	726	1	4
α-helix	727	1
β-strand	728-729	2	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase EZH2	A	protein	229	Homo sapiens	Q15910 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4MI5_1 Histone-lysine N-methyltransferase EZH2 (chains A)
GSLQPCDHPRQPCDSSCPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAV
RECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEF
ISEYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYA
KVMMVNGDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGIEREMEIP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural Context of Disease-Associated Mutations and Putative Mechanism of Autoinhibition Revealed by X-Ray Crystallographic Analysis of the EZH2-SET Domain. Antonysamy, S., Condon, B., Druzina, Z. et al. PLoS One (2013) 8:e84147-e84147. DOI 10.1371/journal.pone.0084147 · PubMed

Other PDB entries of the same protein (UniProt Q15910 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5U5T 1.6 Å, Crystal structure of EED in complex with H3K27Me3 peptide and…
7QK4 1.6 Å, EED in complex with PRC2 allosteric inhibitor compound 22 (MAK683)
7QJG 1.8 Å, EED in complex with PRC2 allosteric inhibitor compound 6
7QJU 1.8 Å, EED in complex with PRC2 allosteric inhibitor compound 7
5H14 1.9 Å, EED in complex with an allosteric PRC2 inhibitor EED666
5H19 1.9 Å, EED in complex with PRC2 allosteric inhibitor EED162
5U62 1.9 Å, Crystal structure of EED in complex with H3K27Me3 peptide and…
4MI0 2.0 Å, Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)
5WUK 2.03 Å, Crystal structure of EED [G255D] in complex with EZH2 peptide and EED226 compound
6LO2 2.21 Å, Crystal structure of EED in complex with EZH2 peptide and compound 11#
5H15 2.27 Å, EED in complex with PRC2 allosteric inhibitor EED709
5H17 2.3 Å, EED in complex with PRC2 allosteric inhibitor EED210

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