8T9G: Automethylated PRC2 dimer

Automethylated PRC2 dimer bound to nucleosome. Determined by electron microscopy at 6.2 Å resolution. Released 25 Sept 2024.

Method: Electron microscopy
Resolution: 6.2 Å
Organisms: Homo sapiens, Xenopus laevis, synthetic construct
Chains: 21
Atoms: 45,911
Mol. weight: 825.69 kDa
Ligands: SAH
Released: 25 Sept 2024

Explore 8T9G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T9G contains 143 α-helices and 261 β-strands across 19 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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	39
α-helix	36-38	3
α-helix	41-42	2
α-helix	45-55	11
α-helix	64-75	12
β-strand	83-84	2	40
α-helix	86-113	28
β-strand	118	1	41
α-helix	121-131	11

Chain B: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	84-104	21
α-helix	112-114	3
α-helix	116-118	3
α-helix	134-146	13
β-strand	158-160	3	1
β-strand	164-165	2	2
β-strand	184-191	8	3
β-strand	203-211	9	3
β-strand	230-232	3	1
α-helix	239-242	4
α-helix	246-248	3
β-strand	249-252	4	3
β-strand	296	1	4
β-strand	297-300	4	3
β-strand	314-318	5	2
β-strand	320	1	4
β-strand	354-358	5	2
β-strand	359-360	2	1
β-strand	429-434	6	5
β-strand	438-443	6	5
α-helix	460-470	11
β-strand	474-475	2	6
β-strand	478-480	3	5
β-strand	485-489	5	5
β-strand	490-491	2	6
α-helix	504-507	4
α-helix	509	1
β-strand	510	1	7
β-strand	513	1	7
β-strand	525-530	6	8
α-helix	540-547	8
β-strand	559-560	2	8
β-strand	566	1	9
β-strand	573	1	9
α-helix	574-575	2
α-helix	576-578	3
α-helix	590-601	12
α-helix	608-624	17
α-helix	629-639	11
α-helix	644-650	7
α-helix	654-665	12
α-helix	671-681	11

Chain C: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	15-21	7
α-helix	26-35	10
α-helix	38-62	25
β-strand	82-85	4	10
β-strand	86	1	11
β-strand	94-97	4	10
α-helix	99-103	5
β-strand	114-115	2	12
β-strand	120-121	2	13
α-helix	172-175	4
α-helix	177-179	3
α-helix	223-227	5
α-helix	237-251	15
α-helix	274-284	11
β-strand	285-286	2	14
β-strand	291-292	2	14
α-helix	336-343	8
α-helix	439-448	10
α-helix	458-462	5
α-helix	470-480	11
α-helix	540-544	5
α-helix	577-580	4
β-strand	583	1	15
α-helix	591-593	3
β-strand	619-623	5	9
β-strand	629-633	5	9
β-strand	637	1	16
β-strand	642-643	2	15
β-strand	649-652	4	13
α-helix	653-666	14
β-strand	671-672	2	13
β-strand	678-681	4	13
β-strand	685-686	2	12
α-helix	688-691	4
β-strand	700-706	7	15
β-strand	711-717	7	15
β-strand	721	1	16
α-helix	735-742	8

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain F: 3 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	82-89	8	11
β-strand	95	1	17
β-strand	101	1	18
β-strand	107	1	19
β-strand	109	1	19
β-strand	112-116	5	18
β-strand	120-126	7	18
α-helix	128-130	3
β-strand	132-139	8	18
β-strand	147-154	8	20
β-strand	161-167	7	20
β-strand	172-175	4	20
β-strand	176	1	21
β-strand	181	1	21
β-strand	193-198	6	22
β-strand	205-210	6	22
β-strand	215-219	5	22
β-strand	224-229	6	22
β-strand	239-241	3	23
β-strand	244	1	24
β-strand	250-253	4	24
β-strand	254-255	2	23
β-strand	261-264	4	24
α-helix	268-278	11
β-strand	293-294	2	22
β-strand	309-315	7	25
β-strand	318-323	6	25
β-strand	327-334	8	25
α-helix	340-342	3
β-strand	350-352	3	25
β-strand	356-357	2	25
β-strand	369-370	2	26
β-strand	376	1	27
β-strand	377-378	2	26
β-strand	379-380	2	28
β-strand	386-388	3	28
β-strand	390	1	27
β-strand	402-404	3	28
β-strand	416-418	3	11
β-strand	424-429	6	11
β-strand	431	1	17
β-strand	433-439	7	11

Chain G: 16 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	83-88	6
α-helix	91-104	14
α-helix	134-145	12
β-strand	158-160	3	50
β-strand	162-165	4	51
β-strand	184-191	8	52
β-strand	203-211	9	52
β-strand	230-232	3	50
α-helix	239-243	5
α-helix	246-247	2
β-strand	248-253	6	52
β-strand	296-300	5	52
β-strand	302	1	53
β-strand	308	1	53
β-strand	314-318	5	51
β-strand	320	1	52
β-strand	354-358	5	51
β-strand	359-360	2	50
β-strand	428-434	7	54
β-strand	438-442	5	54
β-strand	449	1	55
β-strand	456	1	55
α-helix	460-470	11
β-strand	474-478	5	54
β-strand	485-491	7	54
α-helix	503-507	5
α-helix	509	1
β-strand	525-530	6	56
α-helix	541-547	7
β-strand	557-560	4	56
β-strand	566-567	2	57
β-strand	572-573	2	57
α-helix	574-575	2
α-helix	576-578	3
α-helix	590-602	13
α-helix	608-624	17
α-helix	629-650	22
α-helix	653-665	13
α-helix	671-681	11

Chain I: 23 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	20-62	43
α-helix	66-68	3
β-strand	82-84	3	58
β-strand	85-87	3	59
β-strand	95-97	3	58
β-strand	114-115	2	60
β-strand	121	1	39
α-helix	123-125	3
α-helix	139-142	4
α-helix	145-152	8
α-helix	168-178	11
α-helix	222-227	6
α-helix	237-246	10
α-helix	274-284	11
β-strand	285-286	2	61
β-strand	291-292	2	61
α-helix	334-342	9
α-helix	439-451	13
α-helix	456-462	7
α-helix	472-479	8
α-helix	483-484	2
α-helix	501-511	11
α-helix	512-516	5
α-helix	540-544	5
α-helix	577-580	4
α-helix	584-586	3
α-helix	590-593	4
β-strand	621-623	3	57
β-strand	629-631	3	57
β-strand	632	1	62
β-strand	637	1	63
β-strand	642-643	2	64
β-strand	649-651	3	39
α-helix	653-665	13
β-strand	671-673	3	39
β-strand	679-681	3	39
β-strand	685-686	2	60
α-helix	689-691	3
β-strand	693-694	2	65
β-strand	700-707	8	64
β-strand	710-717	8	64
β-strand	721	1	63
β-strand	726	1	62
β-strand	728-729	2	65
α-helix	735-742	8

Chain J: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45	1	41
α-helix	50-76	27
β-strand	80-81	2	40
α-helix	83-92	10
β-strand	96-98	3	42

11 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
Polycomb protein SUZ12	B, G	protein	619	Homo sapiens	Q15022 (AlphaFold model)
Histone-lysine N-methyltransferase EZH2	C, I	protein	753	Homo sapiens	Q15910 (AlphaFold model)
Polycomb protein EED	F, K	protein	441	Homo sapiens	O75530 (AlphaFold model)
Histone-binding protein RBBP4	L, O	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Zinc finger protein AEBP2	M, Y	protein	303	Homo sapiens	Q6ZN18
Histone H3.2	A, W	protein	136	Xenopus laevis	P84233
DNA (226-mer)	H	DNA	215	synthetic construct
Histone H4	J, X	protein	106	Xenopus laevis	P62799
Histone H2A type 1	R, U	protein	133	Xenopus laevis	P06897
Histone H2B 1.1	S, V	protein	123	Xenopus laevis	P02281
DNA (226-mer)	T	DNA	215	synthetic construct
activating methylated peptide	E	protein	12	Homo sapiens

Sequence of entity 1 (B, G), FASTA

>8T9G_1 Polycomb protein SUZ12 (chains B, G)
MVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTN
IKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEV
LLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVK
SYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNR
RLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETN
DKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKL
RIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGAR
IDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLES
EDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDV
NEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDF
NLISIMSIDKAVTKLREMQ

Sequence of entity 2 (C, I), FASTA

>8T9G_2 Histone-lysine N-methyltransferase EZH2 (chains C, I)
SNAGQTGKKSEKGPVACRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQ
EWKQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQ
NFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNAL
GQYNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAE
ELKEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHR
KCNYSFHATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGR
RRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSR
CQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKE
SSIIAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSS
CPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADH
WDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADR
RGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAK
RAIQTGEELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 3 (F, K), FASTA

>8T9G_3 Polycomb protein EED (chains F, K)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Sequence of entity 4 (L, O), FASTA

>8T9G_4 Histone-binding protein RBBP4 (chains L, O)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 5 (M, Y), FASTA

>8T9G_5 Zinc finger protein AEBP2 (chains M, Y)
SNAYTRRYSSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNS
SPDLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGG
CNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRP
HDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPE
DILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKRTLIRKVFNLYL
SKQ

Sequence of entity 6 (A, W), FASTA

>8T9G_6 Histone H3.2 (chains A, W)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 7 (H), FASTA

>8T9G_7 DNA (226-MER) (chains H)
ATCGGGAGCTCCGACCGAATGACATGCATGCATACAGGATGTATATACCTGACACGTGCC
TGGAGACTAGGGAGTAACCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGT
TTAAGCGGTGCTAGAGCTGCCTACGACCAATGGAGCGGCCTCGGCACCGGGATCCCCCAG
CCGCCGGCAGCGCAGCGCCTGACGGGCACACAGTC

Sequence of entity 8 (J, X), FASTA

>8T9G_8 Histone H4 (chains J, X)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGGSSG

Sequence of entity 9 (R, U), FASTA

>8T9G_9 Histone H2A type 1 (chains R, U)
SNAMSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLL
PKCTESSKSAKSK

Sequence of entity 10 (S, V), FASTA

>8T9G_10 Histone H2B 1.1 (chains S, V)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 11 (T), FASTA

>8T9G_11 DNA (226-MER) (chains T)
GACTGTGTGCCCGTCAGACGCTGCGCCGCCGGCGGCCGGAGAATCCCGGTGCCGAGGCCG
CCCTATTGGTCGTAGACAGCCCCAGCACCGCCTAAACGCACGTACGCGCCGTCCCCCGCG
TTTTAACCGCCAAGGGGATTACCCCCCAGTCCCCAGGCACGTGCCAGATATATACATCCC
GTACGCACGCACATCATTCGATCGGAGCTCCCGAT

Sequence of entity 12 (E), FASTA

>8T9G_12 activating methylated peptide (chains E)
XXXXXXXXKXXX

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Primary citation

Activation of automethylated PRC2 by dimerization on chromatin. Sauer, P.V., Pavlenko, E., Cookis, T. et al. Mol Cell (2024) 84:3885-3898.e8. DOI 10.1016/j.molcel.2024.08.025 · PubMed

Other PDB entries of the same protein (UniProt Q15022 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IJ7 2.62 Å, Structure of Hs/AcPRC2 in complex with a pyridone inhibitor
9XZI 2.69 Å, Crystal Structure of the SUZ12-RBBP4-PHF19-EPOP PRC2.1 Subcomplex
4W2R 2.81 Å, Structure of Hs/AcPRC2 in complex with 5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihy…
6NQ3 2.89 Å, Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex
5WAI 2.9 Å, Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex
5HYN 2.95 Å, Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M…
5IJ8 2.99 Å, Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in complex with a pyridone…
7TD5 2.99 Å, Structure of human PRC2-EZH1 containing phosphorylated SUZ12
6B3W 3.05 Å, Structure of Hs/AcPRC2 in complex with 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(…
9KOF 3.07 Å, Structure of human PRC2 with SAH and H3K27me3 peptide
8VMI 3.1 Å, PRC2_AJ119-450 bound to H3K4me3
8VNV 3.1 Å, PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged

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