8VNZ: PRC2_AJ1-450

PRC2_AJ1-450 bound to H3K36me3-modified nucleosome with histone H3 tail disengaged. Determined by electron microscopy at 3.5 Å resolution. Released 15 Jan 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 14,771
Mol. weight: 350.25 kDa
Ligands: SAH
Released: 15 Jan 2025

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

Secondary structure: helices and β-sheets

8VNZ contains 61 α-helices and 114 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: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	84-106	23
α-helix	112-114	3
α-helix	135-145	11
β-strand	157-165	9	1
β-strand	183-184	2	2
β-strand	185-191	7	3
β-strand	192	1	4
α-helix	193-194	2
β-strand	203-207	5	3
β-strand	211-212	2	2
β-strand	230-232	3	1
β-strand	245	1	4
β-strand	249-253	5	3
β-strand	296-300	5	3
β-strand	302	1	5
β-strand	308	1	5
β-strand	314-317	4	1
β-strand	354-361	8	1
β-strand	428-433	6	6
β-strand	442	1	7
β-strand	449	1	8
β-strand	456	1	8
α-helix	460-470	11
β-strand	474-481	8	6
β-strand	484-491	8	6
α-helix	503-505	3
α-helix	509	1
β-strand	525-530	6	9
α-helix	540-542	3
β-strand	557-560	4	9
β-strand	566	1	10
α-helix	572	1
β-strand	573	1	10
α-helix	574-575	2
α-helix	578-580	3
α-helix	590-602	13
α-helix	608-624	17
α-helix	629-650	22
α-helix	653-665	13
α-helix	671-679	9

Chain B: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	142	1	7
α-helix	144-146	3
α-helix	161-164	4

Chain C: 29 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	18-33	16
α-helix	35-62	28
α-helix	66-71	6
α-helix	75-78	4
β-strand	82-86	5	12
β-strand	94-97	4	12
β-strand	99-100	2	14
α-helix	101-103	3
α-helix	106-109	4
β-strand	114-115	2	26
α-helix	138-141	4
α-helix	144-153	10
α-helix	168-175	8
α-helix	221-230	10
α-helix	239-249	11
α-helix	274-283	10
β-strand	285	1	27
β-strand	292	1	27
α-helix	310-312	3
α-helix	329-338	10
α-helix	434-443	10
α-helix	451-457	7
α-helix	463-476	14
α-helix	495-505	11
α-helix	506-510	5
α-helix	511-512	2
α-helix	518-520	3
α-helix	535-538	4
α-helix	572-575	4
β-strand	578	1	28
α-helix	579-581	3
α-helix	605-608	4
α-helix	611-613	3
β-strand	614-618	5	10
β-strand	624-628	5	10
β-strand	632	1	29
β-strand	637-638	2	28
β-strand	644-647	4	30
α-helix	648-661	14
β-strand	673-676	4	30
β-strand	680-681	2	26
α-helix	683-686	4
β-strand	688	1	31
β-strand	695-702	8	28
β-strand	705-712	8	28
β-strand	716	1	29
β-strand	721	1	10
β-strand	723	1	31
β-strand	724-725	2	28
α-helix	730-736	7

Chain L: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	82-83	2	11
β-strand	89-90	2	12
α-helix	94-96	3
β-strand	99-101	3	13
β-strand	111-115	5	13
β-strand	120-121	2	14
β-strand	122-126	5	13
β-strand	132-134	3	13
α-helix	136-137	2
β-strand	138-139	2	14
β-strand	147-154	8	15
β-strand	161-167	7	15
β-strand	171-176	6	15
β-strand	181-187	7	15
β-strand	196-198	3	16
β-strand	205-210	6	16
β-strand	214-219	6	16
β-strand	224-228	5	16
β-strand	239-244	6	17
β-strand	250-255	6	17
β-strand	260-264	5	17
α-helix	268-278	11
α-helix	288-289	2
β-strand	293	1	16
β-strand	309-315	7	18
β-strand	318-323	6	18
β-strand	327-333	7	18
β-strand	350-357	8	18
β-strand	368-370	3	19
β-strand	376-379	4	19
β-strand	386-390	5	19
α-helix	396-398	3
β-strand	402-404	3	19
β-strand	416-418	3	11
β-strand	424-427	4	11
β-strand	435-439	5	11

Chain N: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	6-26	21
β-strand	32-39	8	9
β-strand	48-49	2	20
β-strand	54	1	20
β-strand	62-69	8	20
β-strand	78-86	9	20
β-strand	115-122	8	20
β-strand	131-132	2	21
β-strand	139-141	3	21
β-strand	149-153	5	21
β-strand	171-173	3	21
β-strand	183-185	3	22
β-strand	192-195	4	22
β-strand	202-206	5	22
β-strand	216-217	2	21
β-strand	221-223	3	22
β-strand	230-236	7	23
β-strand	239-247	9	23
β-strand	252-256	5	23
β-strand	267	1	23
β-strand	276-281	6	24
β-strand	288-293	6	24
β-strand	298-302	5	24
β-strand	311-313	3	24
β-strand	320-325	6	25
β-strand	332-337	6	25
β-strand	342-346	5	25
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	25
β-strand	377-382	6	9
β-strand	390-394	5	9
β-strand	398-404	7	9
α-helix	406-408	3

Chain P: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	183-186	4
α-helix	192-208	17
β-strand	219-223	5	32
β-strand	224	1	33
β-strand	229-231	3	1
β-strand	237-241	5	1
β-strand	243	1	33
α-helix	249-251	3
β-strand	252-254	3	1
α-helix	256-258	3
β-strand	264-268	5	32
α-helix	277-280	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polycomb protein SUZ12	A	protein	739	Homo sapiens	Q15022 (AlphaFold model)
Polycomb protein EED	L	protein	441	Homo sapiens	O75530 (AlphaFold model)
Histone-binding protein RBBP4	N	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Histone-lysine N-methyltransferase EZH2	C	protein	746	Homo sapiens	Q15910 (AlphaFold model)
Protein Jumonji	B	protein	449	Homo sapiens	Q92833
Isoform 3 of Zinc finger protein AEBP2	P	protein	301	Homo sapiens	Q6ZN18

Sequence of entity 1 (A), FASTA

>8VNZ_1 Polycomb protein SUZ12 (chains A)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL

Sequence of entity 2 (L), FASTA

>8VNZ_2 Polycomb protein EED (chains L)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Sequence of entity 3 (N), FASTA

>8VNZ_3 Histone-binding protein RBBP4 (chains N)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 4 (C), FASTA

>8VNZ_4 Histone-lysine N-methyltransferase EZH2 (chains C)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH
ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPN
NSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKM
KPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA
PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQ
NFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS
CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK
YMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE
ELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 5 (B), FASTA

>8VNZ_5 Protein Jumonji (chains B)
SKERPKRNIIQKKYDDSDGIPWSEERVVRKVLYLSLKEFKNSQKRQHAEGIAGSLKTVNG
LLGNDQSKGLGPASEQSENEKDDASQVSSTSNDVSSSDFEEGPSRKRPRLQAQRKFAQSQ
PNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYFGSSQD
EEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKEPVQKH
KSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAATHHHPPLHRSAQDLRK
QVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKRELVKDTK
PNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPKSCTKE
VGGRQLREGLQLREGLRNSKRRLEEAHQA

Sequence of entity 6 (P), FASTA

>8VNZ_6 Isoform 3 of Zinc finger protein AEBP2 (chains P)
MYTRRYSSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSP
DLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCN
ASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHD
FFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDI
LPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKRTLIRKVFNLYLSK
Q

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1

Primary citation

Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications. Cookis, T., Lydecker, A., Sauer, P. et al. Nat Struct Mol Biol (2025) 32:393-404. DOI 10.1038/s41594-024-01452-x · 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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