9KOH: Human PRC2-SAH-H3K27me3-C36

Structure of human PRC2-SAH-H3K27me3-C36. Determined by electron microscopy at 3.1 Å resolution. Released 17 Jun 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 7
Atoms: 13,654
Mol. weight: 268.99 kDa
Ligands: SAH, A1EGC
Released: 17 Jun 2026

Explore 9KOH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KOH contains 47 α-helices and 115 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 C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	27	1	10

Chain D: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	82-90	9	1
β-strand	98-101	4	2
α-helix	109-110	2
β-strand	111-116	6	2
β-strand	120-126	7	2
α-helix	128-130	3
β-strand	132-139	8	2
β-strand	147-154	8	12
β-strand	161-167	7	12
β-strand	171-176	6	12
β-strand	181-187	7	12
β-strand	193-198	6	13
β-strand	205-210	6	13
β-strand	215-219	5	13
β-strand	224-229	6	13
β-strand	239-244	6	14
β-strand	250-255	6	14
β-strand	260-264	5	14
α-helix	268-278	11
β-strand	292-294	3	13
β-strand	299-301	3	14
β-strand	309-315	7	15
β-strand	318-323	6	15
β-strand	327-333	7	15
α-helix	340-342	3
β-strand	350-357	8	15
β-strand	367	1	1
β-strand	368-370	3	16
β-strand	376-380	5	16
β-strand	386-390	5	16
β-strand	401-404	4	16
β-strand	415-418	4	1
β-strand	424-428	5	1
β-strand	433-439	7	1

Chain F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	184-201	18
β-strand	211-215	5	22
α-helix	216	1
β-strand	218-223	6	17
β-strand	229-233	5	17
α-helix	242-243	2
β-strand	244-247	4	17
β-strand	256-260	5	22
α-helix	266-269	4
α-helix	270-272	3

Chain I: 15 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	23-33	11
α-helix	35-60	26
β-strand	82-87	6	1
β-strand	94-97	4	1
β-strand	99-100	2	2
α-helix	101-103	3
β-strand	114-115	2	3
β-strand	120-121	2	4
α-helix	144-151	8
α-helix	274-277	4
α-helix	279-283	5
β-strand	286	1	5
β-strand	291	1	5
α-helix	438-447	10
α-helix	451-457	7
α-helix	463-473	11
β-strand	543	1	6
β-strand	556	1	6
β-strand	578	1	7
α-helix	579-581	3
α-helix	611-613	3
β-strand	614-618	5	8
β-strand	624-628	5	8
β-strand	632	1	9
β-strand	639-641	3	7
β-strand	644-645	2	4
β-strand	646-647	2	10
α-helix	650-658	9
β-strand	666-670	5	10
β-strand	673-676	4	10
β-strand	680-681	2	3
α-helix	683-685	3
β-strand	688	1	11
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	1	11

Chain K: 4 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	8-26	19
α-helix	28-30	3
β-strand	32-39	8	21
β-strand	48-50	3	23
β-strand	62-67	6	23
β-strand	77	1	24
β-strand	81-86	6	23
β-strand	204	1	23
β-strand	208	1	24
β-strand	214	1	25
β-strand	217	1	26
β-strand	224-227	4	26
β-strand	228	1	25
β-strand	234-238	5	26
α-helix	246-247	2
β-strand	257-258	2	26
β-strand	267-270	4	27
β-strand	277-281	5	27
β-strand	289-291	3	27
β-strand	301-302	2	26
β-strand	315-318	4	28
β-strand	327-332	6	28
β-strand	337-341	5	28
β-strand	352	1	28
β-strand	361-366	6	29
β-strand	373	1	30
β-strand	374-378	5	29
β-strand	383-384	2	29
β-strand	387	1	30
β-strand	397-398	2	29
β-strand	405-410	6	31
β-strand	417-422	6	31
β-strand	427-431	5	31
α-helix	443-446	4
β-strand	451-455	5	31
β-strand	462-467	6	21
β-strand	474-479	6	21
β-strand	483-489	7	21

Chain O: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	87-104	18
α-helix	112-114	3
α-helix	119-121	3
α-helix	128-131	4
α-helix	137-147	11
β-strand	157-165	9	17
β-strand	183-192	10	18
α-helix	193-194	2
β-strand	203-212	10	18
β-strand	215	1	17
β-strand	229-232	4	17
α-helix	234-237	4
α-helix	239-243	5
β-strand	245-255	11	18
β-strand	294-302	9	18
β-strand	308	1	18
β-strand	313-318	6	17
β-strand	320	1	18
α-helix	348-350	3
β-strand	354-361	8	17
β-strand	428-433	6	19
β-strand	438-443	6	19
β-strand	449	1	20
β-strand	456	1	20
α-helix	460-470	11
β-strand	474-480	7	19
β-strand	485-491	7	19
α-helix	503-507	5
α-helix	509	1
β-strand	525-531	7	21
β-strand	566	1	8
β-strand	573	1	8
α-helix	577-579	3
α-helix	590-600	11
α-helix	609-624	16
α-helix	629-631	3
α-helix	632-647	16
α-helix	653-665	13
α-helix	671-681	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase EZH2	I	protein	754	Homo sapiens	Q15910 (AlphaFold model)
H3K27me3	C, E	protein	10	Homo sapiens
Polycomb protein EED	D	protein	362	Homo sapiens	O75530 (AlphaFold model)
Polycomb protein SUZ12	O	protein	597	Homo sapiens	Q15022 (AlphaFold model)
Zinc finger protein AEBP2	F	protein	106	Homo sapiens	Q6ZN18 (AlphaFold model)
RB binding protein 4, chromatin remodeling factor,Histone-binding protein RBBP4	K	protein	492	Homo sapiens	E9PNS6, Q09028

Sequence of entity 1 (I), FASTA

>9KOH_1 Histone-lysine N-methyltransferase EZH2 (chains I)
HHHHHHHHMGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILER
TEILNQEWKQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYS
WSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFV
ELVNALGQYNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFP
DKGTAEELKEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKY
DCFLHPFHATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGG
RRRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANS
RCQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVK
ESSIIAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDS
SCPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAAD
HWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEAD
RRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFA
KRAIQTGEELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 2 (C, E), FASTA

>9KOH_2 H3K27me3 (chains C, E)
TKAARKSAPA

Sequence of entity 3 (D), FASTA

>9KOH_3 Polycomb protein EED (chains D)
YSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYV
DADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFH
PRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHS
LKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLI
LSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLAL
GNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDR
LR

Sequence of entity 4 (O), FASTA

>9KOH_4 Polycomb protein SUZ12 (chains O)
FLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVDDMLSKVEKMK
GEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKKRKDVSCPIRQ
VPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVTRPGRREFNGM
INGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQEMEEC
PISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAKPLATRNSESL
HQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEAR
DDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSINECYDGSYAGNPQD
IHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLESEDGEVEQQRTYSSGHNRLY
FHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDVNEGEKEVMKLWNLHVMKHG
FIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSIDKAVTKLR

Sequence of entity 5 (F), FASTA

>9KOH_5 Zinc finger protein AEBP2 (chains F)
PHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMP
EDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQK

Sequence of entity 6 (K), FASTA

>9KOH_6 RB binding protein 4, chromatin remodeling factor,Histone-binding protein RBBP4 (chains K)
KEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSI
HRLVLGTHTSDEQNHLVIASVQLPNKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTH
ALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHY
DSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHP
SKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVD
AKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNC
LSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGT
DRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNI
MQVWQMAENIYN

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
A1EGC	2-[2-[[4-[(8-chloranyl-1,7-naphthyridin-2-yl)amino]cyclohexyl]methylamino]pyrim…	C24 H28 Cl N7 O2	1

Primary citation

Structure of human PRC2 with SAH and H3K27me3 peptide. Gao, H., Cao, T., Liu, Y. et al. To be published.

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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