9DCH: Single-stranded RNA-mediated PRC2 dimer

Single-stranded RNA-mediated PRC2 dimer. Determined by electron microscopy at 3.4 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 13
Atoms: 24,433
Mol. weight: 674.68 kDa
Ligands: ZN
Released: 12 Mar 2025

Explore 9DCH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DCH contains 102 α-helices and 229 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: 19 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	23-60	38
β-strand	82-85	4	1
β-strand	94-97	4	1
β-strand	99-100	2	2
α-helix	101-103	3
β-strand	114-115	2	3
β-strand	119-121	3	4
β-strand	274	1	5
β-strand	276	1	5
α-helix	280-283	4
β-strand	286	1	6
β-strand	291	1	6
α-helix	337-346	10
α-helix	431-433	3
α-helix	439-452	14
α-helix	457-462	6
α-helix	468-481	14
α-helix	522-524	3
α-helix	540-543	4
β-strand	548	1	7
β-strand	561	1	7
α-helix	562-563	2
β-strand	567	1	8
α-helix	577-580	4
β-strand	583	1	9
α-helix	591-595	5
α-helix	610-613	4
β-strand	619-623	5	10
β-strand	629-633	5	10
β-strand	642-645	4	9
β-strand	648-651	4	4
α-helix	653-664	12
β-strand	672-673	2	4
β-strand	679-681	3	4
β-strand	685-686	2	3
α-helix	688-690	3
β-strand	693	1	11
β-strand	700-707	8	9
β-strand	710-717	8	9
α-helix	721-722	2
α-helix	725	1
β-strand	726	1	10
α-helix	727	1
β-strand	728	1	11

Chain B: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	82-106	25
α-helix	132-134	3
α-helix	135-138	4
β-strand	158	1	12
β-strand	184	1	13
β-strand	185-188	4	14
α-helix	201-202	2
β-strand	211	1	13
β-strand	232	1	12
β-strand	250-253	4	14
β-strand	297-298	2	14
β-strand	313-318	6	15
β-strand	354-359	6	15
β-strand	429	1	16
β-strand	430	1	17
β-strand	432	1	18
β-strand	442	1	17
β-strand	449	1	19
β-strand	456	1	19
α-helix	461-469	9
β-strand	475-476	2	18
β-strand	486	1	16
β-strand	489-490	2	18
α-helix	503-506	4
α-helix	509	1
β-strand	525-530	6	20
α-helix	540-543	4
β-strand	557-560	4	20
β-strand	565-566	2	10
α-helix	572	1
β-strand	573-574	2	10
α-helix	575	1
α-helix	590-601	12
α-helix	608-624	17
α-helix	629-642	14
α-helix	644-650	7
α-helix	653-661	9
α-helix	664-666	3
α-helix	671-688	18

Chain C: 4 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	30
β-strand	99-101	3	31
α-helix	110-111	2
β-strand	113-115	3	31
β-strand	122-124	3	31
β-strand	125-127	3	32
β-strand	131-133	3	32
β-strand	137	1	31
β-strand	138-139	2	2
β-strand	151-154	4	33
β-strand	161-165	5	33
β-strand	172-176	5	33
β-strand	181-186	6	33
β-strand	193-198	6	34
β-strand	205-210	6	34
β-strand	214-219	6	34
β-strand	224-229	6	34
β-strand	231	1	35
β-strand	234	1	35
β-strand	242-244	3	36
β-strand	250-253	4	36
β-strand	262-264	3	36
α-helix	268-278	11
α-helix	288-289	2
β-strand	292-294	3	34
β-strand	299	1	36
β-strand	309-311	3	37
β-strand	319	1	37
β-strand	322-323	2	37
β-strand	327-332	6	37
α-helix	340-342	3
β-strand	351-357	7	37
β-strand	368-370	3	38
β-strand	377-380	4	38
β-strand	386-389	4	38
β-strand	402-404	3	38
β-strand	416-418	3	30
β-strand	424-427	4	30
β-strand	435-439	5	30

Chain D: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	4-26	23
β-strand	32-39	8	20
α-helix	43-44	2
β-strand	64-67	4	21
β-strand	80-84	5	21
β-strand	117-120	4	21
β-strand	132	1	22
β-strand	139-143	5	22
β-strand	148-153	6	22
β-strand	172-174	3	22
β-strand	180	1	23
β-strand	184	1	24
β-strand	193-196	4	24
β-strand	197	1	23
β-strand	202-205	4	24
α-helix	210-211	2
β-strand	216-217	2	22
β-strand	221-223	3	24
β-strand	230-235	6	25
β-strand	242-247	6	25
β-strand	250-251	2	25
β-strand	254-256	3	25
β-strand	267	1	25
β-strand	278-279	2	26
β-strand	289-292	4	26
β-strand	299-301	3	26
β-strand	312	1	26
β-strand	320-323	4	27
β-strand	332-337	6	27
β-strand	342-346	5	27
α-helix	356-361	6
β-strand	368-370	3	27
β-strand	377-382	6	20
β-strand	389-394	6	20
β-strand	399-404	6	20
α-helix	407-409	3

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	143-147	5
α-helix	160-163	4

Chain F: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	194-209	16
β-strand	219-220	2	28
β-strand	224-229	6	29
β-strand	239-243	5	29
β-strand	254	1	29
α-helix	256-261	6
β-strand	267-268	2	28
α-helix	277-280	4
α-helix	289-291	3

Chain H: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	23-60	38
β-strand	82	1	39
β-strand	85	1	40
α-helix	92-93	2
β-strand	94	1	40
β-strand	97	1	39
β-strand	114-115	2	41
β-strand	274	1	42
β-strand	276	1	42
α-helix	280-283	4
α-helix	337-346	10
α-helix	431-433	3
α-helix	439-452	14
α-helix	457-462	6
α-helix	468-481	14
α-helix	522-524	3
α-helix	540-543	4
β-strand	548	1	43
β-strand	561	1	43
α-helix	562-565	4
β-strand	567	1	8
α-helix	577-580	4
β-strand	583	1	44
α-helix	610-613	4
β-strand	619-623	5	45
β-strand	629-633	5	45
β-strand	637	1	46
β-strand	642-645	4	44
β-strand	649-651	3	47
α-helix	653-664	12
β-strand	671-673	3	47
β-strand	679-681	3	47
β-strand	685-686	2	41
α-helix	688-690	3
β-strand	700-707	8	44
β-strand	710-717	8	44
β-strand	721	1	46
α-helix	722	1
β-strand	726	1	45
α-helix	731-733	3

Chain I: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	82-106	25
α-helix	132-134	3
α-helix	135-138	4
β-strand	158	1	48
β-strand	184	1	49
β-strand	185-188	4	50
α-helix	201-202	2
β-strand	211	1	49
β-strand	232	1	48
β-strand	250-253	4	50
β-strand	313-318	6	51
α-helix	319-321	3
β-strand	354-359	6	51
β-strand	429-433	5	52
β-strand	442	1	52
β-strand	443	1	53
β-strand	449	1	54
β-strand	456	1	54
α-helix	460-462	3
α-helix	464-470	7
β-strand	474-476	3	52
β-strand	486-491	6	52
α-helix	503-505	3
α-helix	509	1
β-strand	525-530	6	55
α-helix	540-543	4
β-strand	557-560	4	55
β-strand	565-566	2	45
α-helix	572	1
β-strand	573-574	2	45
α-helix	575	1
α-helix	576-579	4
α-helix	590-601	12
α-helix	608-624	17
α-helix	629-650	22
α-helix	653-661	9
α-helix	664-666	3
α-helix	671-688	18

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
TERRAmut RNA	G	RNA	10	Homo sapiens
Isoform 2 of Histone-lysine N-methyltransferase EZH2	A, H	protein	750	Homo sapiens	Q15910 (AlphaFold model)
Polycomb protein SUZ12	B, I	protein	727	Homo sapiens	Q15022 (AlphaFold model)
RBAP48	D, K	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Zinc finger protein AEBP2	F, M	protein	294	Homo sapiens	Q6ZN18 (AlphaFold model)
Protein Jumonji	E, L	protein	332	Homo sapiens	Q92833
Polycomb protein EED	C, J	protein	441	Homo sapiens	O75530

Sequence of entity 1 (G), FASTA

>9DCH_1 TERRAmut RNA (chains G)
UGAGUGUGAG

Sequence of entity 2 (A, H), FASTA

>9DCH_2 Isoform 2 of Histone-lysine N-methyltransferase EZH2 (chains A, H)
GQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEWK
QRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNFM
VEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQY
NDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEELK
EKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHRKCN
YSFHATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRG
RLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQT
PIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSI
IAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPC
VIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDS
KNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGK
VYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAI
QTGEELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 3 (B, I), FASTA

>9DCH_3 Polycomb protein SUZ12 (chains B, I)
MAPQKHGGGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSAAAAAGAAVLPVK
KPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTF
KVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVC
HKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLF
RVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLD
GEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAP
IAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQF
LYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSIN
ECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLESEDGEVE
QQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDVNEGEKE
VMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIM
SIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEKALETDSVSGVSK
QSKKQKL

Sequence of entity 4 (D, K), FASTA

>9DCH_4 RBAP48 (chains D, K)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 5 (F, M), FASTA

>9DCH_5 Zinc finger protein AEBP2 (chains F, M)
SSDGEPLSRMDSEDSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQ
ACFNSSPDLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFK
CVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRR
SLPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLL
HWMPEDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR

Sequence of entity 6 (E, L), FASTA

>9DCH_6 Protein Jumonji (chains E, L)
QSQPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYFGS
SQDEEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKEPV
QKHKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAATHHHPPLHRSAQD
LRKQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKRELVK
DTKPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPKSC
TKEVGGRQLREGLQLREGLRNSKRRLEEAHQA

Sequence of entity 7 (C, J), FASTA

>9DCH_7 Polycomb protein EED (chains C, J)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14

Primary citation

RNA-induced PRC2 inhibition depends on the sequence of bound RNA. Song, J., Yao, L., Gooding, A.R. et al. bioRxiv (2025). DOI 10.1101/2024.08.29.610323 · PubMed

Other PDB entries of the same protein (UniProt Q15910 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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)
7QJG 1.8 Å, EED in complex with PRC2 allosteric inhibitor compound 6
7QJU 1.8 Å, EED in complex with PRC2 allosteric inhibitor compound 7
5H14 1.9 Å, EED in complex with an allosteric PRC2 inhibitor EED666
5H19 1.9 Å, EED in complex with PRC2 allosteric inhibitor EED162
5U62 1.9 Å, Crystal structure of EED in complex with H3K27Me3 peptide and…
4MI0 2.0 Å, Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)
4MI5 2.0 Å, Crystal structure of the EZH2 SET domain
5WUK 2.03 Å, Crystal structure of EED [G255D] in complex with EZH2 peptide and EED226 compound
6LO2 2.21 Å, Crystal structure of EED in complex with EZH2 peptide and compound 11#
5H15 2.27 Å, EED in complex with PRC2 allosteric inhibitor EED709

Browse structure collections

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