6C23: PRC2

Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State. Determined by electron microscopy at 3.9 Å resolution. Released 24 Jan 2018.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 12
Atoms: 13,440
Mol. weight: 639.41 kDa
Released: 24 Jan 2018

Explore 6C23 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C23 contains 43 α-helices and 108 β-strands across 12 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	432-433	2	1
β-strand	444	1	2
α-helix	460-469	10
β-strand	474-480	7	1
β-strand	486-491	6	1
β-strand	529-530	2	3
α-helix	544-547	4

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	108-111	4

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	18-60	43
β-strand	82-83	2	33
β-strand	85-87	3	10
β-strand	96-97	2	33
β-strand	101	1	12
β-strand	114	1	9
β-strand	120-121	2	8
α-helix	145-152	8
α-helix	168-179	12
α-helix	221-230	10
α-helix	238-246	9

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	143	1	2
α-helix	144-149	6

Chain K: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	274-277	4
α-helix	279-283	5
β-strand	285-286	2	4
β-strand	291-292	2	4
α-helix	426-428	3
α-helix	436-447	12
α-helix	453-457	5
α-helix	463-476	14
α-helix	535-538	4
α-helix	541-543	3
α-helix	572-575	4
β-strand	578	1	5
α-helix	605-608	4
β-strand	614-618	5	6
β-strand	624-628	5	6
β-strand	632	1	7
β-strand	637-640	4	5
β-strand	644-646	3	8
α-helix	648-661	14
β-strand	666-668	3	8
β-strand	674-676	3	8
β-strand	680	1	9
α-helix	683-686	4
β-strand	696-701	6	5
β-strand	706-711	6	5
β-strand	716	1	7
β-strand	721	1	6
α-helix	733-734	2

Chain L: 5 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	82-84	3	10
β-strand	88-90	3	10
α-helix	95-96	2
β-strand	98-101	4	11
α-helix	109-110	2
β-strand	111-116	6	11
β-strand	120-126	7	11
α-helix	128-130	3
β-strand	132	1	11
β-strand	137-139	3	11
β-strand	140	1	12
β-strand	147	1	13
β-strand	151-154	4	13
β-strand	161-167	7	13
β-strand	171-175	5	13
β-strand	176	1	14
β-strand	181	1	14
β-strand	185-186	2	13
β-strand	195-196	2	15
β-strand	205-209	5	15
β-strand	215-219	5	15
β-strand	224-229	6	15
β-strand	239-244	6	16
β-strand	250-255	6	16
β-strand	260-264	5	16
α-helix	268-278	11
α-helix	282-284	3
β-strand	292-294	3	15
β-strand	300-301	2	16
β-strand	312-315	4	17
β-strand	318-321	4	17
β-strand	327-333	7	17
β-strand	350-357	8	17
β-strand	370	1	18
β-strand	376-377	2	18
β-strand	389-390	2	18
β-strand	413-418	6	10
β-strand	424-429	6	10
β-strand	433	1	10
β-strand	436-439	4	10

Chain M: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	565-566	2	6
α-helix	572	1
β-strand	573-574	2	6
α-helix	575	1
α-helix	577-579	3
α-helix	592-602	11
α-helix	608-624	17
α-helix	629-650	22
α-helix	653-663	11
α-helix	671-681	11

Chain N: 5 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	5-27	23
α-helix	28-30	3
β-strand	32-39	8	3
β-strand	48-49	2	19
β-strand	54	1	20
β-strand	61-62	2	21
β-strand	63	1	20
β-strand	65-67	3	19
β-strand	78-80	3	22
β-strand	81-83	3	19
β-strand	86-87	2	21
β-strand	116	1	19
β-strand	120-122	3	22
β-strand	139-142	4	23
β-strand	150-153	4	23
α-helix	154-156	3
α-helix	166-167	2
β-strand	184-185	2	24
β-strand	193-194	2	24
β-strand	204-205	2	24
β-strand	230-235	6	25
β-strand	242-247	6	25
β-strand	252-256	5	25
β-strand	267-269	3	25
β-strand	276	1	26
β-strand	280-281	2	27
β-strand	288-292	5	27
β-strand	293	1	26
β-strand	298-302	5	27
β-strand	309-313	5	27
β-strand	320-323	4	28
β-strand	332-337	6	28
β-strand	342-346	5	28
α-helix	356-361	6
β-strand	366-370	5	28
β-strand	377-382	6	3
β-strand	389-394	6	3
β-strand	398-404	7	3

4 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	A, M, Q	protein	739	Homo sapiens	Q15022 (AlphaFold model)
Protein Jumonji	E	protein	348	Homo sapiens	Q92833 (AlphaFold model)
Histone-lysine N-methyltransferase EZH2	C, K	protein	746	Homo sapiens	Q15910 (AlphaFold model)
Polycomb protein EED	L	protein	441	Homo sapiens	O75530 (AlphaFold model)
Histone-binding protein RBBP4	N	protein	425	Homo sapiens	Q09028
JARID2-substrate	O	protein	7	Homo sapiens
Zinc finger protein AEBP2	P	protein	295	Homo sapiens	Q6ZN18
SUZ12	Z	protein	135	Homo sapiens
Protein Jumonji	B	protein	345	Homo sapiens	Q92833 (AlphaFold model)

Sequence of entity 1 (A, M, Q), FASTA

>6C23_1 Polycomb protein SUZ12 (chains A, M, Q)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL

Sequence of entity 2 (E), FASTA

>6C23_2 Protein Jumonji (chains E)
SNARKRPRLQAQRKFAQSQPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLC
LRGSPALPNSMVYFGSSQDEEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNG
HVFNGSSRSTREKEPVQKHKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKG
LAATHHHPPLHRSAQDLRKQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATV
TKGAVTYTKAKRELVKDTKPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGP
AVNGLKVSGRLNPKSCTKEVGGRQLREGLQLREGLRNSKRRLEEAHQA

Sequence of entity 3 (C, K), FASTA

>6C23_3 Histone-lysine N-methyltransferase EZH2 (chains C, K)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH
ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPN
NSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKM
KPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA
PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQ
NFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS
CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK
YMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE
ELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 4 (L), FASTA

>6C23_4 Polycomb protein EED (chains L)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Sequence of entity 5 (N), FASTA

>6C23_5 Histone-binding protein RBBP4 (chains N)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 6 (O), FASTA

>6C23_6 JARID2-substrate (chains O)
AAARKFA

Sequence of entity 7 (P), FASTA

>6C23_7 Zinc finger protein AEBP2 (chains P)
MSSDGEPLSRMDSEDSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQC
QACFNSSPDLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPF
KCVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRR
RSLPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLL
LHWMPEDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR

Sequence of entity 8 (Z), FASTA

>6C23_8 SUZ12 (chains Z)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXX

Sequence of entity 9 (B), FASTA

>6C23_9 Protein Jumonji (chains B)
RKRPRLQAQRKFAQSQPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRG
SPALPNSMVYFGSSQDEEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVF
NGSSRSTREKEPVQKHKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAA
THHHPPLHRSAQDLRKQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKG
AVTYTKAKRELVKDTKPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVN
GLKVSGRLNPKSCTKEVGGRQLREGLQLREGLRNSKRRLEEAHQA

Primary citation

Structures of human PRC2 with its cofactors AEBP2 and JARID2. Kasinath, V., Faini, M., Poepsel, S. et al. Science (2018) 359:940-944. DOI 10.1126/science.aar5700 · 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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