8VMI: PRC2_AJ119-450

PRC2_AJ119-450 bound to H3K4me3. Determined by electron microscopy at 3.1 Å resolution. Released 15 Jan 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 9
Atoms: 14,940
Mol. weight: 526.05 kDa
Ligands: ZN
Released: 15 Jan 2025

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

Secondary structure: helices and β-sheets

8VMI contains 62 α-helices and 124 β-strands across 8 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: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	82-90	9	1
β-strand	96-101	6	2
α-helix	110	1
β-strand	111-117	7	2
β-strand	120-126	7	2
α-helix	128-130	3
β-strand	132-139	8	2
β-strand	147-154	8	3
β-strand	161-167	7	3
β-strand	172-176	5	3
β-strand	181-186	6	3
β-strand	193-199	7	4
β-strand	202-210	9	4
β-strand	215-219	5	4
β-strand	225-229	5	4
β-strand	239-244	6	5
β-strand	250-255	6	5
β-strand	260-264	5	5
α-helix	268-278	11
α-helix	282-284	3
β-strand	292-294	3	4
β-strand	299-301	3	5
β-strand	309-315	7	6
β-strand	318-323	6	6
β-strand	327-333	7	6
β-strand	350-357	8	6
β-strand	369-370	2	7
β-strand	376-380	5	7
β-strand	386-390	5	7
β-strand	404	1	7
α-helix	412	1
β-strand	413-418	6	1
β-strand	424-429	6	1
β-strand	433-439	7	1

Chain C: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	16-60	45
α-helix	66-68	3
β-strand	81-87	7	1
α-helix	92-93	2
β-strand	94-98	5	1
β-strand	99-100	2	2
α-helix	101-103	3
β-strand	114-115	2	28
α-helix	169-179	11
α-helix	221-230	10
α-helix	237-245	9
α-helix	274-284	11
β-strand	285	1	29
β-strand	292	1	29
α-helix	329-338	10
α-helix	434-447	14
α-helix	451-457	7
α-helix	463-476	14
α-helix	497-509	13
α-helix	518-520	3
α-helix	535-538	4
β-strand	543	1	30
β-strand	556	1	30
α-helix	572-575	4
β-strand	578	1	31
α-helix	605-608	4
α-helix	611-613	3
β-strand	614-618	5	9
β-strand	624-628	5	9
β-strand	632	1	32
β-strand	637-638	2	31
β-strand	644-647	4	33
α-helix	648-660	13
β-strand	666-668	3	33
β-strand	673-676	4	33
β-strand	680-681	2	28
α-helix	683-686	4
β-strand	688	1	34
β-strand	695-702	8	31
β-strand	705-712	8	31
β-strand	716	1	32
α-helix	720	1
β-strand	721	1	9
α-helix	722	1
β-strand	723	1	34
β-strand	724	1	31
α-helix	730-737	8

Chain F: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	140-141	2	15
α-helix	145-150	6
α-helix	158-161	4

Chain I: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	27	1	33
α-helix	36-39	4

Chain L: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	559-560	2	8
β-strand	566	1	9
β-strand	573	1	9
α-helix	576-579	4
α-helix	590-601	12
α-helix	608-624	17
α-helix	633-650	18
α-helix	653-660	8
α-helix	671-681	11

Chain N: 9 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	5-26	22
α-helix	28-30	3
β-strand	32-39	8	8
β-strand	48-49	2	17
β-strand	54	1	18
β-strand	62-65	4	18
β-strand	66-67	2	17
β-strand	77-78	2	19
β-strand	82-86	5	18
β-strand	115-117	3	18
β-strand	122-123	2	19
β-strand	130-133	4	20
β-strand	136-142	7	20
β-strand	149-153	5	20
α-helix	154-156	3
α-helix	161-162	2
β-strand	171-173	3	20
β-strand	180-185	6	21
β-strand	192-197	6	21
β-strand	202-206	5	21
β-strand	216-217	2	20
β-strand	221-223	3	21
β-strand	230	1	22
β-strand	235	1	23
β-strand	242-243	2	23
β-strand	246	1	24
β-strand	247	1	22
β-strand	252	1	24
β-strand	255-256	2	23
β-strand	269	1	24
β-strand	276	1	25
β-strand	280-281	2	26
β-strand	288-292	5	26
β-strand	293	1	25
β-strand	298-302	5	26
α-helix	303-305	3
β-strand	312-313	2	26
β-strand	320-325	6	27
α-helix	326	1
β-strand	332-337	6	27
β-strand	342-346	5	27
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	27
β-strand	377-382	6	8
β-strand	389-394	6	8
β-strand	398-404	7	8
α-helix	406-408	3

Chain P: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	174-177	4
α-helix	183-185	3
α-helix	192-209	18
β-strand	219-223	5	35
β-strand	224-232	9	11
β-strand	237-243	7	11
α-helix	246-248	3
β-strand	252-255	4	11
α-helix	256-258	3
β-strand	264-268	5	35
α-helix	277-280	4

Chain T: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	83-106	24
α-helix	112-114	3
α-helix	116-118	3
α-helix	135-146	12
β-strand	164	1	10
β-strand	165	1	11
β-strand	183-184	2	12
β-strand	185-192	8	13
β-strand	203-207	5	13
β-strand	211-212	2	12
β-strand	215	1	10
α-helix	217-218	2
β-strand	229	1	11
α-helix	239-244	6
β-strand	245-253	9	13
β-strand	296-300	5	13
β-strand	302	1	14
β-strand	308	1	14
β-strand	313-318	6	11
β-strand	354-359	6	11
β-strand	427-434	8	15
β-strand	438-444	7	15
β-strand	449	1	16
β-strand	456	1	16
α-helix	460-470	11
β-strand	474-475	2	15
β-strand	478-481	4	15
β-strand	484-491	8	15
α-helix	503-507	5
α-helix	509	1
β-strand	525-530	6	8
α-helix	540-542	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polycomb protein EED	A	protein	441	Homo sapiens	O75530 (AlphaFold model)
Histone H3.1	B	protein	6	Homo sapiens	P68431 (AlphaFold model)
Polycomb protein SUZ12	L, T	protein	739	Homo sapiens	Q15022 (AlphaFold model)
Histone-binding protein RBBP4	N	protein	425	Homo sapiens	Q09028 (AlphaFold model)
EZH2	C	protein	746	Homo sapiens	Q15910
Protein Jumonji	F	protein	1246	Homo sapiens	Q92833
Isoform 3 of Zinc finger protein AEBP2	P	protein	301	Homo sapiens	Q6ZN18
Histone H3.1t	I	protein	18	Homo sapiens	Q16695

Sequence of entity 1 (A), FASTA

>8VMI_1 Polycomb protein EED (chains A)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Sequence of entity 2 (B), FASTA

>8VMI_2 Histone H3.1 (chains B)
ARTKQT

Sequence of entity 3 (L, T), FASTA

>8VMI_3 Polycomb protein SUZ12 (chains L, T)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL

Sequence of entity 4 (N), FASTA

>8VMI_4 Histone-binding protein RBBP4 (chains N)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 5 (C), FASTA

>8VMI_5 EZH2 (chains C)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH
ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPN
NSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKM
KPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA
PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQ
NFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS
CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK
YMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE
ELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 6 (F), FASTA

>8VMI_6 Protein Jumonji (chains F)
MSKERPKRNIIQKKYDDSDGIPWSEERVVRKVLYLSLKEFKNSQKRQHAEGIAGSLKTVN
GLLGNDQSKGLGPASEQSENEKDDASQVSSTSNDVSSSDFEEGPSRKRPRLQAQRKFAQS
QPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYFGSSQ
DEEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKEPVQK
HKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAATHHHPPLHRSAQDLR
KQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKRELVKDT
KPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPKSCTK
EVGGRQLREGLQLREGLRNSKRRLEEAHQAEKPQSPPKKMKGAAGPAEGPGKKAPAERGL
LNGHVKKEVPERSLERNRPKRATAGKSTPGRQAHGKADSASCENRSTSQPESVHKPQDSG
KAEKGGGKAGWAAMDEIPVLRPSAKEFHDPLIYIESVRAQVEKFGMCRVIPPPDWRPECK
LNDEMRFVTQIQHIHKLGRRWGPNVQRLACIKKHLKSQGITMDELPLIGGCELDLACFFR
LINEMGGMQQVTDLKKWNKLADMLRIPRTAQDRLAKLQEAYCQYLLSYDSLSPEEHRRLE
KEVLMEKEILEKRKGPLEGHTENDHHKFHPLPRFEPKNGLIHGVAPRNGFRSKLKEVGQA
QLKTGRRRLFAQEKEVVKEEEEDKGVLNDFHKCIYKGRSVSLTTFYRTARNIMSMCFSKE
PAPAEIEQEYWRLVEEKDCHVAVHCGKVDTNTHGSGFPVGKSEPFSRHGWNLTVLPNNTG
SILRHLGAVPGVTIPWLNIGMVFSTSCWSRDQNHLPYIDYLHTGADCIWYCIPAEEENKL
EDVVHTLLQANGTPGLQMLESNVMISPEVLCKEGIKVHRTVQQSGQFVVCFPGSFVSKVC
CGYSVSETVHFATTQWTSMGFETAKEMKRRHIAKPFSMEKLLYQIAQAEAKKENGPTLST
ISALLDELRDTELRQRRQLFEAGLHSSARYGSHDGSSTVADGKKKPRKWLQLETSERRCQ
ICQHLCYLSMVVQENENVVFCLECALRHVEKQKSCRGLKLMYRYDEEQIISLVNQICGKV
SGKNGSIENCLSKPTPKRGPRKRATVDVPPSRLSASSSSKSASSSS

Sequence of entity 7 (P), FASTA

>8VMI_7 Isoform 3 of Zinc finger protein AEBP2 (chains P)
MYTRRYSSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSP
DLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCN
ASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHD
FFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDI
LPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKRTLIRKVFNLYLSK
Q

Sequence of entity 8 (I), FASTA

>8VMI_8 Histone H3.1t (chains I)
ARKSAPATGGVKKPHRYR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

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 O75530 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5U69 1.28 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-d…
5U8F 1.34 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-i…
5U8A 1.45 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl…
6SFB 1.52 Å, EED in complex with a triazolopyrimidine
3K26 1.58 Å, Complex structure of EED and trimethylated H3K4
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)
7P3C 1.61 Å, EED in complex with compound 4
6V3Y 1.63 Å, Crystal structure of EED in complex with PALI1-K1219me3 peptide
5U6D 1.64 Å, Polycomb protein EED in complex with inhibitor: 2-[4-(4-{(3S,4R)-4-(dimethylamino)-1-[(2-…
6V3X 1.7 Å, Crystal structure of EED in complex with PALI1-K1241me3 peptide
5TTW 1.74 Å, Crystal Structure of EED in Complex with UNC4859

Browse structure collections

About this viewer

MolViewer shows 8VMI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.