9KOF: Human PRC2 with SAH and H3K27me3 peptide

Structure of human PRC2 with SAH and H3K27me3 peptide. Determined by electron microscopy at 3.07 Å resolution. Released 17 Jun 2026.

Method: Electron microscopy
Resolution: 3.07 Å
Organism: Homo sapiens
Chains: 7
Atoms: 13,225
Mol. weight: 254.84 kDa
Ligands: SAH
Released: 17 Jun 2026

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

Secondary structure: helices and β-sheets

9KOF contains 52 α-helices and 113 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: 17 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	19-33	15
α-helix	37-61	25
β-strand	99-100	2	1
α-helix	101-103	3
β-strand	114-115	2	2
β-strand	120-121	2	3
α-helix	130-132	3
α-helix	144-147	4
α-helix	274-277	4
α-helix	279-283	5
β-strand	286	1	4
β-strand	291	1	4
α-helix	438-441	4
α-helix	454-457	4
β-strand	459	1	5
β-strand	461	1	5
α-helix	463-474	12
β-strand	543	1	6
β-strand	556	1	6
α-helix	572-575	4
β-strand	579	1	7
α-helix	580-581	2
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	644-647	4	3
α-helix	648-658	11
β-strand	666-670	5	3
β-strand	673-676	4	3
β-strand	680-681	2	2
α-helix	683-685	3
β-strand	688	1	10
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	10

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	26	1	3

Chain D: 6 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	82-89	8	11
β-strand	98-101	4	12
α-helix	109-110	2
β-strand	111-116	6	12
β-strand	122-126	5	12
α-helix	128-130	3
β-strand	132	1	12
β-strand	136	1	12
β-strand	138-139	2	1
β-strand	147-154	8	13
β-strand	161-167	7	13
β-strand	171	1	14
β-strand	173-176	4	13
β-strand	181-184	4	13
β-strand	187	1	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	239-243	5	16
β-strand	250-255	6	16
β-strand	262-264	3	16
α-helix	268-277	10
α-helix	288-289	2
β-strand	292-294	3	15
β-strand	299	1	16
β-strand	309-315	7	17
β-strand	318-323	6	17
β-strand	327-333	7	17
α-helix	340-342	3
β-strand	350-357	8	17
β-strand	368-370	3	18
β-strand	376-379	4	18
α-helix	385	1
β-strand	386	1	19
β-strand	387-390	4	18
β-strand	404	1	19
β-strand	415-418	4	11
β-strand	424-428	5	11
β-strand	433-439	7	11

Chain F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	400-417	18
β-strand	427-431	5	26
β-strand	433-439	7	20
β-strand	445-450	6	20
α-helix	451	1
β-strand	460-463	4	20
α-helix	469-471	3
β-strand	472-476	5	26
α-helix	482-485	4
α-helix	486-488	3

Chain G: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	539-552	14
α-helix	560-562	3
α-helix	575-579	5
α-helix	585-594	10
α-helix	604	1
β-strand	605-608	4	20
α-helix	682-685	4
β-strand	744	1	21
β-strand	750	1	22
β-strand	756	1	22
β-strand	761-766	6	20
β-strand	768	1	21
α-helix	796-798	3
β-strand	802-809	8	20
β-strand	876-882	7	23
β-strand	885-891	7	23
β-strand	897	1	24
β-strand	904	1	24
α-helix	908-918	11
β-strand	922-928	7	23
β-strand	933-939	7	23
α-helix	951-955	5
α-helix	957	1
β-strand	974-979	6	25
β-strand	1014	1	8
β-strand	1021	1	8
α-helix	1038-1049	12
α-helix	1057-1072	16
α-helix	1077-1079	3
α-helix	1080-1090	11
α-helix	1092-1098	7
α-helix	1101-1113	13
α-helix	1119-1129	11

Chain H: 7 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	415-433	19
α-helix	435-437	3
β-strand	439-446	8	25
β-strand	455-457	3	27
β-strand	469-474	6	27
α-helix	483-484	2
β-strand	485-493	9	27
β-strand	500-503	4	27
β-strand	511-513	3	28
β-strand	520-523	4	28
α-helix	529	1
β-strand	530-534	5	28
α-helix	542-543	2
β-strand	553-554	2	28
β-strand	561-566	6	29
β-strand	573-578	6	29
β-strand	585-587	3	29
β-strand	597-598	2	28
β-strand	611-614	4	30
β-strand	623-628	6	30
β-strand	633-637	5	30
β-strand	648	1	30
α-helix	656	1
β-strand	657	1	31
β-strand	661-662	2	32
β-strand	669	1	33
β-strand	670-671	2	32
β-strand	672-673	2	34
β-strand	674	1	31
β-strand	678-680	3	34
β-strand	683	1	33
β-strand	693-695	3	34
β-strand	701-706	6	35
β-strand	713-718	6	35
β-strand	723-727	5	35
α-helix	739-742	4
β-strand	749-751	3	35
β-strand	758-763	6	25
β-strand	770-775	6	25
β-strand	779-785	7	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase EZH2	A	protein	718	Homo sapiens	Q15910 (AlphaFold model)
H3K27me3	C, E	protein	7	Homo sapiens
Polycomb protein EED	D	protein	370	Homo sapiens	O75530 (AlphaFold model)
Polycomb protein SUZ12	G	protein	597	Homo sapiens	Q15022 (AlphaFold model)
Zinc finger protein AEBP2	F	protein	106	Homo sapiens	Q6ZN18 (AlphaFold model)
Histone-binding protein RBBP4	H	protein	407	Homo sapiens	Q09028

Sequence of entity 1 (A), FASTA

>9KOF_1 Histone-lysine N-methyltransferase EZH2 (chains A)
RVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEWKQRRIQPVHILTSVSSL
RGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDE
VLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQYNDDDDDDDGDDPEERE
EKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEELKEKYKELTEQQLPGALP
PECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFHATPNTYKRKNTETALDN
KPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPNNSSRPSTPTINVLESKD
TDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKMKPNIEPPENVEWSGAEA
SMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPAPAEDVDTPPRKKKRKHR
LWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEKFCQCSSECQNRF
PGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLA
PSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDA
TRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRYSQADALK

Sequence of entity 2 (C, E), FASTA

>9KOF_2 H3K27me3 (chains C, E)
AARKSAP

Sequence of entity 3 (D), FASTA

>9KOF_3 Polycomb protein EED (chains D)
HHHHHHHHYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGE
IRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGN
AINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKI
MSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDC
VRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMD
FWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDD
ASIWRWDRLR

Sequence of entity 4 (G), FASTA

>9KOF_4 Polycomb protein SUZ12 (chains G)
FLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVDDMLSKVEKMK
GEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKKRKDVSCPIRQ
VPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVTRPGRREFNGM
INGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQEMEEC
PISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAKPLATRNSESL
HQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEAR
DDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSINECYDGSYAGNPQD
IHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLESEDGEVEQQRTYSSGHNRLY
FHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDVNEGEKEVMKLWNLHVMKHG
FIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSIDKAVTKLR

Sequence of entity 5 (F), FASTA

>9KOF_5 Zinc finger protein AEBP2 (chains F)
PHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMP
EDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQK

Sequence of entity 6 (H), FASTA

>9KOF_6 Histone-binding protein RBBP4 (chains H)
KEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSI
HRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINH
EGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGL
SWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLF
GSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDL
RNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGP
PELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYN

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	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

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