5HYN: Histone-lysine N-methyltransferase EZH2

Name: PDB 5HYN: Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide
Published: 2016-05-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide. Determined by X-ray diffraction at 2.95 Å resolution. Released 11 May 2016.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Homo sapiens
Chains: 20
Atoms: 35,028
Mol. weight: 586.82 kDa
Ligands: SAH, ZN
Released: 11 May 2016

Explore 5HYN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HYN contains 157 α-helices and 228 β-strands across 16 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: 27 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	12-62	51
α-helix	73	1
α-helix	75-76	2
β-strand	82-87	6	1
α-helix	91-93	3
β-strand	94-97	4	1
α-helix	98	1
β-strand	99-101	3	2
α-helix	105-109	5
β-strand	114-115	2	3
β-strand	120-121	2	3
α-helix	123-125	3
β-strand	128	1	4
α-helix	135-138	4
α-helix	144-152	9
β-strand	157	1	4
α-helix	168-181	14
α-helix	221-230	10
α-helix	237-248	12
α-helix	274-284	11
β-strand	285	1	5
β-strand	292	1	5
α-helix	332-343	12
α-helix	426-428	3
α-helix	434-447	14
α-helix	451-458	8
α-helix	463-474	12
α-helix	535-538	4
β-strand	543	1	6
β-strand	556	1	6
α-helix	557-558	2
α-helix	572-575	4
β-strand	578	1	7
α-helix	611-613	3
β-strand	614-618	5	8
β-strand	624-628	5	8
β-strand	632	1	9
β-strand	637-640	4	7
β-strand	643-647	5	3
α-helix	648-660	13
β-strand	666-668	3	3
β-strand	673-681	9	3
α-helix	683-686	4
α-helix	687	1
β-strand	688-689	2	7
β-strand	695-702	8	7
β-strand	705-712	8	7
β-strand	716	1	9
α-helix	720	1
β-strand	721	1	8
α-helix	722	1
β-strand	723-724	2	7

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	82-90	9	1
β-strand	96-101	6	2
α-helix	106	1
β-strand	112-117	6	2
β-strand	120-127	8	2
β-strand	131-140	10	2
β-strand	147-154	8	10
β-strand	161-167	7	10
β-strand	172-176	5	10
β-strand	181-186	6	10
β-strand	193-198	6	11
β-strand	205-210	6	11
β-strand	215-219	5	11
β-strand	224-228	5	11
β-strand	239-244	6	12
β-strand	250-255	6	12
β-strand	260-264	5	12
α-helix	268-279	12
α-helix	288-289	2
β-strand	292-293	2	11
β-strand	299-301	3	12
β-strand	309-315	7	13
β-strand	318-323	6	13
β-strand	327-333	7	13
α-helix	340-342	3
β-strand	350-357	8	13
β-strand	368-370	3	14
β-strand	376-380	5	14
β-strand	386-390	5	14
β-strand	402-404	3	14
β-strand	413-418	6	1
β-strand	424-429	6	1
β-strand	433-439	7	1

Chain C: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	566	1	8
β-strand	573	1	8
α-helix	585-586	2
α-helix	590-601	12
α-helix	610-624	15
α-helix	631-649	19
α-helix	653-665	13
α-helix	672-683	12

Chains D, I and O: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	27	1	3

Chain F: 28 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	12-62	51
α-helix	65-68	4
α-helix	73	1
α-helix	75-76	2
β-strand	82-87	6	15
β-strand	94-97	4	15
α-helix	98	1
β-strand	99-101	3	16
α-helix	102-103	2
β-strand	114-115	2	17
β-strand	120-121	2	17
α-helix	123-125	3
β-strand	128	1	18
α-helix	145-152	8
β-strand	157	1	18
α-helix	168-180	13
α-helix	223-230	8
α-helix	237-247	11
α-helix	274-277	4
α-helix	279-284	6
β-strand	285	1	19
β-strand	292	1	19
α-helix	329-342	14
α-helix	425-427	3
α-helix	434-446	13
α-helix	451-458	8
α-helix	463-474	12
α-helix	535-538	4
β-strand	543	1	20
β-strand	556	1	20
α-helix	572-575	4
β-strand	578	1	21
α-helix	579-581	3
α-helix	605-608	4
α-helix	611-613	3
β-strand	614-618	5	22
β-strand	624-628	5	22
β-strand	632	1	23
β-strand	637-640	4	21
β-strand	643-647	5	17
α-helix	648-661	14
β-strand	666-668	3	17
β-strand	673-681	9	17
α-helix	683-686	4
α-helix	687	1
β-strand	688-689	2	21
β-strand	695-702	8	21
β-strand	705-712	8	21
β-strand	716	1	23
α-helix	720	1
β-strand	721	1	22
α-helix	722	1
β-strand	723-724	2	21

Chain G: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	82-90	9	15
β-strand	96-101	6	16
α-helix	106	1
α-helix	110	1
β-strand	111-117	7	16
β-strand	120-126	7	16
α-helix	128-130	3
β-strand	132-140	9	16
β-strand	147-154	8	24
β-strand	161-167	7	24
β-strand	172-176	5	24
β-strand	181-186	6	24
β-strand	193-198	6	25
β-strand	205-210	6	25
β-strand	215-219	5	25
β-strand	224-229	6	25
β-strand	239-244	6	26
β-strand	250-255	6	26
β-strand	260-264	5	26
α-helix	268-279	12
α-helix	288-289	2
β-strand	292-294	3	25
β-strand	299-301	3	26
β-strand	309-315	7	27
β-strand	318-323	6	27
β-strand	327-333	7	27
α-helix	340-342	3
β-strand	350-357	8	27
β-strand	368-370	3	28
β-strand	376-380	5	28
β-strand	386-390	5	28
β-strand	401-404	4	28
β-strand	413-418	6	15
β-strand	424-429	6	15
β-strand	433-439	7	15

Chain H: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	566	1	22
α-helix	572	1
β-strand	573	1	22
α-helix	574-575	2
α-helix	576-578	3
α-helix	586-589	4
α-helix	590-601	12
α-helix	608-624	17
α-helix	631-649	19
α-helix	653-665	13
α-helix	672-683	12

Chain K: 25 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	14-62	49
β-strand	82-87	6	29
β-strand	93-97	5	29
α-helix	98	1
β-strand	99-101	3	30
α-helix	102-103	2
β-strand	114-115	2	31
β-strand	120-121	2	31
β-strand	128	1	32
α-helix	145-152	8
β-strand	157	1	32
α-helix	168-179	12
α-helix	220-230	11
α-helix	237-246	10
α-helix	261-263	3
α-helix	274-277	4
α-helix	279-284	6
β-strand	285	1	33
β-strand	292	1	33
α-helix	333-343	11
α-helix	426-428	3
α-helix	434-446	13
α-helix	451-458	8
α-helix	463-475	13
α-helix	477-478	2
α-helix	535-539	5
β-strand	543	1	34
β-strand	556	1	34
α-helix	572-575	4
β-strand	578	1	35
α-helix	605-608	4
α-helix	611-613	3
β-strand	614-618	5	36
β-strand	624-628	5	36
β-strand	632	1	37
β-strand	637-640	4	35
β-strand	643-647	5	31
α-helix	648-661	14
β-strand	666-668	3	31
β-strand	673-681	9	31
α-helix	683-686	4
α-helix	687	1
β-strand	688-689	2	35
β-strand	695-702	8	35
β-strand	705-712	8	35
β-strand	716	1	37
α-helix	720	1
β-strand	721	1	36
α-helix	722	1
β-strand	723-724	2	35

6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase EZH2	A, F, K, Q	protein	746	Homo sapiens	Q15910 (AlphaFold model)
Polycomb protein EED	B, G, L, R	protein	367	Homo sapiens	O75530 (AlphaFold model)
Polycomb protein SUZ12	C, H, M, S	protein	129	Homo sapiens	Q15022 (AlphaFold model)
H3K27M	D, I, O, T	protein	13	Homo sapiens	P68431 (AlphaFold model)
JARID2 K116me3	E, J, P, U	protein	12	Homo sapiens	Q92833

Sequence of entity 1 (A, F, K, Q), FASTA

>5HYN_1 Histone-lysine N-methyltransferase EZH2 (chains A, F, K, Q)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH
ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPN
NSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKM
KPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA
PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQ
NFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS
CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK
YMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE
ELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 2 (B, G, L, R), FASTA

>5HYN_2 Polycomb protein EED (chains B, G, L, R)
GSKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRL
LQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAIN
ELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSC
GMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRW
LGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQ
KMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASI
WRWDRLR

Sequence of entity 3 (C, H, M, S), FASTA

>5HYN_3 Polycomb protein SUZ12 (chains C, H, M, S)
GSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDVNEGEKEVMKL
WNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSIDK
AVTKLREMQ

Sequence of entity 4 (D, I, O, T), FASTA

>5HYN_4 H3K27M (chains D, I, O, T)
ATKAARMSAPATG

Sequence of entity 5 (E, J, P, U), FASTA

>5HYN_5 JARID2 K116me3 (chains E, J, P, U)
RLQAQRKFAQSQ

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	4
ZN	Zinc ion	Zn	32

Primary citation

Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2. Justin, N., Zhang, Y., Tarricone, C. et al. Nat Commun (2016) 7:11316-11316. DOI 10.1038/ncomms11316 · 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

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