6U4Y: EZH2-EED Complex in an Oligomeric State

Crystal Structure of an EZH2-EED Complex in an Oligomeric State. Determined by X-ray diffraction at 2.91 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 2.91 Å
Organism: Homo sapiens
Chains: 6
Atoms: 12,736
Mol. weight: 203.66 kDa
Released: 8 Jul 2020

Explore 6U4Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U4Y contains 48 α-helices and 102 β-strands across 6 chains. 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, 3 β-strands

Element	Residues	Length	Sheet
α-helix	13-60	48
α-helix	65-68	4
β-strand	82-87	6	1
α-helix	92-93	2
β-strand	94-97	4	1
β-strand	99-101	3	2
α-helix	102-103	2
α-helix	144-151	8
α-helix	168-179	12
α-helix	222-230	9
α-helix	232-234	3
α-helix	239-248	10

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	13-60	48
β-strand	65	1	3
α-helix	66-68	3
β-strand	82-87	6	4
α-helix	91-93	3
β-strand	94-97	4	4
β-strand	99-101	3	5
α-helix	102-107	6
β-strand	112-113	2	6
β-strand	118-119	2	6
α-helix	144-151	8
α-helix	168-178	11
α-helix	221-230	10
α-helix	232-234	3
α-helix	237-247	11

Chain C: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-61	44
α-helix	65-68	4
β-strand	82-87	6	7
α-helix	92-93	2
β-strand	94-97	4	7
β-strand	99-101	3	8
α-helix	102-107	6
α-helix	145-151	7
α-helix	168-178	11
α-helix	221-230	10
α-helix	232-234	3
α-helix	237-248	12

Chain D: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	82-90	9	1
β-strand	96-101	6	2
α-helix	106	1
α-helix	110-111	2
β-strand	112-117	6	2
β-strand	120-126	7	2
α-helix	128-130	3
β-strand	132-140	9	2
β-strand	147-154	8	9
β-strand	161-167	7	9
β-strand	172-176	5	9
β-strand	181-186	6	9
β-strand	193-198	6	10
β-strand	205-210	6	10
β-strand	215-219	5	10
β-strand	224-229	6	10
β-strand	239-244	6	11
β-strand	250-255	6	11
β-strand	260-264	5	11
α-helix	268-278	11
β-strand	292-294	3	10
β-strand	299-301	3	11
β-strand	311-315	5	12
β-strand	318-322	5	12
β-strand	327-333	7	12
α-helix	340-342	3
β-strand	350-357	8	12
β-strand	369-370	2	13
β-strand	376-380	5	13
β-strand	386-390	5	13
α-helix	396-398	3
β-strand	402-404	3	13
β-strand	413-418	6	1
β-strand	424-429	6	1
β-strand	433-439	7	1

Chain E: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	82-90	9	4
β-strand	96-101	6	5
β-strand	105	1	3
α-helix	106	1
α-helix	110-111	2
β-strand	112-117	6	5
β-strand	120-126	7	5
α-helix	128-130	3
β-strand	132-140	9	5
β-strand	147-154	8	14
β-strand	161-167	7	14
β-strand	171-176	6	14
β-strand	181-187	7	14
β-strand	193-198	6	15
β-strand	205-210	6	15
β-strand	215-219	5	15
β-strand	224-229	6	15
β-strand	239-244	6	16
β-strand	250-255	6	16
β-strand	260-264	5	16
α-helix	268-278	11
α-helix	290-291	2
β-strand	292-294	3	15
β-strand	299-301	3	16
β-strand	311-315	5	17
β-strand	318-322	5	17
β-strand	327-333	7	17
α-helix	340-342	3
β-strand	350-357	8	17
β-strand	369-370	2	18
β-strand	376-380	5	18
β-strand	386-390	5	18
α-helix	396-398	3
α-helix	400-401	2
β-strand	402-404	3	18
α-helix	412	1
β-strand	413-418	6	4
β-strand	424-429	6	4
β-strand	433-439	7	4

Chain F: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	82-90	9	7
β-strand	96-101	6	8
α-helix	105-106	2
β-strand	107	1	19
β-strand	109	1	19
α-helix	110-111	2
β-strand	112-117	6	8
β-strand	120-126	7	8
α-helix	128-130	3
β-strand	132-140	9	8
β-strand	147-155	9	20
β-strand	160-167	8	20
β-strand	172-176	5	20
β-strand	181-186	6	20
β-strand	193-198	6	21
β-strand	205-210	6	21
β-strand	215-219	5	21
β-strand	224-229	6	21
β-strand	239-244	6	22
β-strand	250-255	6	22
β-strand	260-264	5	22
α-helix	268-279	12
β-strand	292-294	3	21
β-strand	299-301	3	22
β-strand	311-315	5	23
β-strand	318-323	6	23
β-strand	327-333	7	23
α-helix	340-342	3
β-strand	350-357	8	23
β-strand	369-370	2	24
β-strand	376-380	5	24
β-strand	386-390	5	24
α-helix	396-398	3
β-strand	402-404	3	24
β-strand	413-418	6	7
β-strand	424-429	6	7
β-strand	433-439	7	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase EZH2	A, B, C	protein	224	Homo sapiens	Q15910 (AlphaFold model)
Polycomb protein EED	D, E, F	protein	366	Homo sapiens	O75530 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6U4Y_1 Histone-lysine N-methyltransferase EZH2 (chains A, B, C)
SGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILSSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNGSSGSDKIFEAISSMFPDKGTAEELKEKYKELTEQQLPGALP

Sequence of entity 2 (D, E, F), FASTA

>6U4Y_2 Polycomb protein EED (chains D, E, F)
GSCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLL
QSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINE
LKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCG
MDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWL
GDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQK
MLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIW
RWDRLR

Primary citation

A partially disordered region connects gene repression and activation functions of EZH2. Jiao, L., Shubbar, M., Yang, X. et al. Proc Natl Acad Sci U S A (2020) 117:16992-17002. DOI 10.1073/pnas.1914866117 · 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)
4MI5 2.0 Å, Crystal structure of the EZH2 SET domain
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

Browse structure collections

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