8EQV: PRC2

Cryo-EM structure of PRC2 in complex with the long isoform of AEBP2. Determined by electron microscopy at 3.64 Å resolution. Released 31 Jul 2024.

Method: Electron microscopy
Resolution: 3.64 Å
Organism: Homo sapiens
Chains: 5
Atoms: 13,974
Mol. weight: 321.19 kDa
Released: 31 Jul 2024

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

Secondary structure: helices and β-sheets

8EQV contains 44 α-helices and 111 β-strands across 5 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: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-26	23
α-helix	28-30	3
β-strand	32-39	8	1
β-strand	48-49	2	2
β-strand	54	1	2
β-strand	62-69	8	2
β-strand	77-86	10	2
β-strand	115-123	9	2
β-strand	130-132	3	3
β-strand	140-143	4	3
β-strand	149-152	4	3
β-strand	171-173	3	3
β-strand	180-184	5	4
β-strand	192-197	6	4
β-strand	202-206	5	4
β-strand	217	1	3
β-strand	221-223	3	4
β-strand	230-235	6	5
β-strand	242-247	6	5
β-strand	251-256	6	5
β-strand	267-270	4	5
β-strand	276-281	6	6
β-strand	288-293	6	6
β-strand	298-302	5	6
β-strand	313	1	6
β-strand	320-325	6	7
β-strand	333-337	5	7
β-strand	344	1	7
α-helix	356-361	6
β-strand	368	1	7
β-strand	377-382	6	1
β-strand	389-394	6	1
β-strand	398-404	7	1
α-helix	406-409	4

Chain B: 14 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	84-89	6
α-helix	91-106	16
α-helix	112-114	3
α-helix	116-121	6
α-helix	134-146	13
β-strand	158-165	8	9
β-strand	186-192	7	25
α-helix	193-195	3
β-strand	203-207	5	25
β-strand	215	1	9
β-strand	230-232	3	9
β-strand	245-247	3	25
β-strand	249-252	4	25
β-strand	296	1	26
β-strand	297-300	4	25
β-strand	302	1	27
β-strand	308	1	27
β-strand	313-318	6	9
β-strand	320	1	26
β-strand	354-360	7	9
α-helix	424-426	3
β-strand	429-434	6	28
β-strand	437-441	5	28
α-helix	460-470	11
β-strand	474	1	29
β-strand	477-479	3	28
β-strand	486-489	4	28
β-strand	491	1	29
β-strand	526	1	1
β-strand	528	1	30
β-strand	530	1	1
β-strand	557	1	30
β-strand	566	1	22
β-strand	573	1	22
α-helix	590-600	11
α-helix	608-624	17
α-helix	631-642	12
α-helix	644-650	7
α-helix	653-665	13
α-helix	671-684	14

Chain C: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	400-417	18
β-strand	427-431	5	8
β-strand	434-440	7	9
β-strand	445-449	5	9
β-strand	461-463	3	9
α-helix	465-467	3
β-strand	472-476	5	8
α-helix	477-479	3
α-helix	482-485	4

Chain D: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	23-60	38
β-strand	82-85	4	18
β-strand	86-87	2	10
β-strand	94-97	4	18
β-strand	99-100	2	11
α-helix	101	1
β-strand	114-115	2	19
β-strand	120-121	2	20
α-helix	169-180	12
α-helix	220-223	4
α-helix	225-228	4
α-helix	239-246	8
α-helix	275-282	8
β-strand	286	1	21
β-strand	291	1	21
α-helix	329-339	11
α-helix	436-447	12
α-helix	453-457	5
α-helix	463-474	12
α-helix	572-575	4
α-helix	605-608	4
α-helix	611-613	3
β-strand	614-618	5	22
β-strand	624-628	5	22
β-strand	632	1	23
β-strand	637-640	4	24
β-strand	644-646	3	20
α-helix	648-658	11
β-strand	666-668	3	20
β-strand	674-676	3	20
β-strand	680-681	2	19
α-helix	683-685	3
β-strand	695-702	8	24
β-strand	705-712	8	24
β-strand	716	1	23

Chain E: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	82-89	8	10
β-strand	98-101	4	11
β-strand	107	1	12
β-strand	109	1	12
α-helix	110-111	2
β-strand	112-116	5	11
β-strand	120-127	8	11
α-helix	128-130	3
β-strand	131-139	9	11
β-strand	147-154	8	13
β-strand	161-167	7	13
β-strand	171-176	6	13
β-strand	181-187	7	13
β-strand	193-198	6	14
β-strand	205-210	6	14
β-strand	215-219	5	14
β-strand	224-229	6	14
β-strand	239-244	6	15
β-strand	250-255	6	15
β-strand	260-264	5	15
α-helix	268-277	10
α-helix	282-284	3
α-helix	288-290	3
β-strand	292-294	3	14
β-strand	299-301	3	15
β-strand	309-315	7	16
β-strand	318-323	6	16
β-strand	327-334	8	16
β-strand	350-357	8	16
β-strand	368-370	3	17
β-strand	376-379	4	17
β-strand	387-390	4	17
β-strand	402	1	17
β-strand	413-418	6	10
β-strand	424-429	6	10
β-strand	433-439	7	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Zinc finger protein AEBP2	C	protein	517	Homo sapiens	Q6ZN18 (AlphaFold model)
Polycomb protein EED	E	protein	441	Homo sapiens	O75530 (AlphaFold model)
Histone-lysine N-methyltransferase EZH2	D	protein	746	Homo sapiens	Q15910 (AlphaFold model)
Polycomb protein SUZ12	B	protein	739	Homo sapiens	Q15022

Sequence of entity 1 (A), FASTA

>8EQV_1 Histone-binding protein RBBP4 (chains A)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 2 (C), FASTA

>8EQV_2 Zinc finger protein AEBP2 (chains C)
MAAAITDMADLEELSRLSPLPPGSPGSAARGRAEPPEEEEEEEEEEEEAEAEAVAALLLN
GGSGGGGGGGGGGVGGGEAETMSEPSPESASQAGEDEDEEEDDEEEEDESSSSGGGEEES
SAESLVGSSGGSSSDETRSLSPGAASSSSGDGDGKEGLEEPKGPRGSQGGGGGGSSSSSV
VSSGGDEGYGTGGGGSSATSGGRRGSLEMSSDGEPLSRMDSEDSISSTIMDVDSTISSGR
STPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHIRSIHVDGQRGGVFVCLWK
GCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQQNSSK
VSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHDFFDAQTLDAIRHRAICFNLSAHIE
SLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDILPDVWVNESERHQLKTKVVHLSKL
PKDTALLLDPNIYRTMPQKRLKRTLIRKVFNLYLSKQ

Sequence of entity 3 (E), FASTA

>8EQV_3 Polycomb protein EED (chains E)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Sequence of entity 4 (D), FASTA

>8EQV_4 Histone-lysine N-methyltransferase EZH2 (chains D)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH
ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPN
NSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKM
KPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA
PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQ
NFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS
CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK
YMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE
ELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 5 (B), FASTA

>8EQV_5 Polycomb protein SUZ12 (chains B)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL

Primary citation

Auto-inhibition of PRC2 by the broadly expressed long isoform of AEBP2. Mucha, M., Lai, Z., McKenzie, N.J. et al. EMBO J (2025). DOI 10.1038/s44318-025-00616-9 · PubMed

Other PDB entries of the same protein (UniProt Q09028 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4R7A 1.85 Å, Crystal Structure of RBBP4 bound to PHF6 peptide
7M40 1.88 Å, Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4)
2XU7 1.9 Å, Structural basis for RbAp48 binding to FOG-1
5XXQ 1.9 Å, Crystal structure of RBBP4: ZNF827 and its function in telomere
6BW4 2.0 Å, Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide
9V5M 2.1 Å, The crystal structure of RBBP4-H3 complex
5Y1U 2.14 Å, Crystal structure of RBBP4 bound to AEBP2 RRK motif
4PBZ 2.15 Å, Structure of the human RbAp48-MTA1(670-695) complex
6BW3 2.2 Å, Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide
8TX8 2.2 Å, Crystal Structure of RBBP4 bound to ZNF512B peptide
3GFC 2.3 Å, Crystal Structure of Histone-binding protein RBBP4
5VTB 2.4 Å, Crystal structure of RBBP4 bound to BCL11a peptide

Browse structure collections

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