8FYH: G4 RNA-mediated PRC2 dimer

G4 RNA-mediated PRC2 dimer. Determined by electron microscopy at 3.4 Å resolution. Released 4 Oct 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 13
Atoms: 25,638
Mol. weight: 929.37 kDa
Ligands: ZN
Released: 4 Oct 2023

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

Secondary structure: helices and β-sheets

8FYH contains 118 α-helices and 235 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: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	23-60	38
β-strand	82-85	4	23
β-strand	94-97	4	23
β-strand	99-100	2	10
α-helix	101-103	3
β-strand	114-115	2	24
β-strand	120-121	2	25
α-helix	169-177	9
α-helix	224-230	7
α-helix	240-249	10
α-helix	274-277	4
α-helix	279-283	5
β-strand	286	1	26
β-strand	291	1	26
α-helix	336-344	9
α-helix	431-433	3
α-helix	439-452	14
α-helix	456-462	7
α-helix	468-478	11
α-helix	540-543	4
β-strand	548	1	27
β-strand	561	1	27
α-helix	562-565	4
β-strand	567	1	28
β-strand	570	1	29
α-helix	577-580	4
β-strand	583	1	30
α-helix	584-586	3
β-strand	606	1	29
α-helix	610-613	4
β-strand	619-623	5	8
β-strand	629-633	5	8
β-strand	637	1	31
β-strand	642-645	4	30
β-strand	649-652	4	25
α-helix	653-663	11
β-strand	671-673	3	25
β-strand	678-681	4	25
β-strand	685-686	2	24
α-helix	688-690	3
β-strand	693	1	32
β-strand	700-707	8	30
β-strand	710-717	8	30
β-strand	721	1	31
α-helix	725	1
β-strand	726	1	8
α-helix	727	1
β-strand	728	1	32
β-strand	729	1	30
α-helix	731-733	3
α-helix	738-741	4

Chain B: 20 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	81-104	24
α-helix	112-114	3
α-helix	116-118	3
α-helix	132-134	3
α-helix	135-139	5
α-helix	140-145	6
β-strand	157-159	3	1
β-strand	163-164	2	1
β-strand	184	1	2
β-strand	185-192	8	3
α-helix	193	1
β-strand	203-206	4	3
β-strand	211	1	2
β-strand	232-233	2	1
β-strand	245-253	9	3
β-strand	296-300	5	3
β-strand	302	1	4
β-strand	308	1	4
β-strand	313-318	6	1
β-strand	320	1	3
β-strand	354-361	8	1
β-strand	428-434	7	5
β-strand	438-441	4	5
β-strand	449	1	6
β-strand	456	1	6
α-helix	460-469	10
β-strand	474-478	5	5
β-strand	485-491	7	5
α-helix	503-506	4
α-helix	509	1
β-strand	525-530	6	7
α-helix	536-538	3
α-helix	540-543	4
β-strand	557-560	4	7
β-strand	566	1	8
β-strand	573	1	8
α-helix	574-575	2
α-helix	576-578	3
α-helix	590-601	12
α-helix	608-624	17
α-helix	629-642	14
α-helix	644-650	7
α-helix	653-665	13
α-helix	671-688	18

Chain C: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	9
α-helix	95	1
β-strand	96-101	6	10
α-helix	106	1
β-strand	111-117	7	10
β-strand	120-126	7	10
α-helix	128-130	3
β-strand	133-139	7	10
β-strand	149-155	7	11
β-strand	160-166	7	11
β-strand	172-176	5	11
β-strand	181-186	6	11
β-strand	193-198	6	12
β-strand	205-210	6	12
β-strand	215-219	5	12
β-strand	224-228	5	12
β-strand	241-244	4	13
β-strand	250-254	5	13
β-strand	260-264	5	13
α-helix	268-278	11
α-helix	288-289	2
β-strand	292-293	2	12
β-strand	309-315	7	14
β-strand	318-323	6	14
β-strand	327-334	8	14
β-strand	350-357	8	14
β-strand	369-370	2	15
β-strand	376-379	4	15
β-strand	386-390	5	15
β-strand	402-404	3	15
β-strand	415-418	4	9
β-strand	424-428	5	9
β-strand	434-439	6	9

Chain D: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	4-26	23
β-strand	32-39	8	7
β-strand	47-54	8	16
β-strand	62-69	8	16
β-strand	77-86	10	16
β-strand	117-123	7	16
β-strand	132	1	17
β-strand	139-143	5	17
β-strand	148-153	6	17
α-helix	161-162	2
β-strand	172-174	3	17
β-strand	180	1	18
β-strand	184-185	2	18
β-strand	193-197	5	18
β-strand	201-205	5	18
β-strand	217-218	2	17
β-strand	221-223	3	18
β-strand	230-235	6	19
β-strand	242-247	6	19
β-strand	253-256	4	19
β-strand	267	1	19
β-strand	276	1	20
β-strand	280-281	2	21
β-strand	288-292	5	21
β-strand	293	1	20
β-strand	298-302	5	21
β-strand	312-313	2	21
β-strand	320-325	6	22
β-strand	332-337	6	22
β-strand	342-346	5	22
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	22
β-strand	377-382	6	7
β-strand	389-394	6	7
β-strand	398-404	7	7
α-helix	406-409	4

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	143-148	6
α-helix	160-163	4

Chain F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	183-185	3
α-helix	193-209	17
β-strand	219-223	5	33
β-strand	224-229	6	34
β-strand	230-231	2	1
β-strand	239-243	5	34
β-strand	252-254	3	34
α-helix	256-261	6
β-strand	264-268	5	33
α-helix	269-271	3
α-helix	277-280	4

Chain G: 22 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	23-60	38
β-strand	82-85	4	57
β-strand	94-97	4	57
β-strand	99-100	2	44
α-helix	101-103	3
β-strand	114-115	2	58
β-strand	120-121	2	58
α-helix	169-177	9
α-helix	224-230	7
α-helix	240-249	10
α-helix	274-277	4
α-helix	279-283	5
β-strand	286	1	59
β-strand	291	1	59
α-helix	336-344	9
α-helix	431-433	3
α-helix	439-452	14
α-helix	456-462	7
α-helix	468-478	11
α-helix	540-543	4
β-strand	548	1	60
β-strand	561	1	60
α-helix	562-565	4
β-strand	567	1	28
β-strand	570	1	61
α-helix	577-580	4
β-strand	583	1	62
β-strand	606	1	61
α-helix	610-613	4
β-strand	619-623	5	42
β-strand	629-633	5	42
β-strand	637	1	63
β-strand	642-645	4	62
β-strand	648-651	4	58
α-helix	653-663	11
β-strand	671-673	3	58
β-strand	679-686	8	58
α-helix	688-690	3
β-strand	693	1	64
β-strand	700-707	8	62
β-strand	710-717	8	62
β-strand	721	1	63
α-helix	725	1
β-strand	726	1	42
α-helix	727	1
β-strand	728	1	64
β-strand	729	1	62
α-helix	731-733	3
α-helix	738-741	4

Chain H: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	81-104	24
α-helix	112-114	3
α-helix	116-118	3
α-helix	135-139	5
α-helix	140-145	6
β-strand	157-159	3	35
β-strand	163-164	2	35
β-strand	184	1	36
β-strand	185-192	8	37
α-helix	193	1
β-strand	203-206	4	37
β-strand	211	1	36
β-strand	232-233	2	35
β-strand	245-253	9	37
β-strand	296-300	5	37
β-strand	302	1	38
β-strand	308	1	38
β-strand	313-318	6	35
β-strand	320	1	37
β-strand	354-361	8	35
β-strand	428-434	7	39
β-strand	438-443	6	39
β-strand	449	1	40
β-strand	456	1	40
α-helix	460-469	10
β-strand	474-478	5	39
β-strand	485-491	7	39
α-helix	503-507	5
α-helix	509	1
β-strand	525-530	6	41
α-helix	536-538	3
α-helix	540-543	4
β-strand	557-560	4	41
β-strand	566	1	42
α-helix	572	1
β-strand	573	1	42
α-helix	574-575	2
α-helix	590-601	12
α-helix	608-624	17
α-helix	629-642	14
α-helix	644-650	7
α-helix	653-665	13
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
Polycomb protein SUZ12	B, H	protein	739	Homo sapiens	Q15022 (AlphaFold model)
Polycomb protein EED	C, I	protein	441	Homo sapiens	O75530 (AlphaFold model)
Histone-binding protein RBBP4	D, J	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Histone-lysine N-methyltransferase EZH2	A, G	protein	751	Homo sapiens	Q15910 (AlphaFold model)
protein Jumonji isoform X3	E, K	protein	1238	Homo sapiens	Q92833
Zinc finger protein AEBP2	F, L	protein	517	Homo sapiens	Q6ZN18
G4 RNA	M	RNA	24	Homo sapiens

Sequence of entity 1 (B, H), FASTA

>8FYH_1 Polycomb protein SUZ12 (chains B, H)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL

Sequence of entity 2 (C, I), FASTA

>8FYH_2 Polycomb protein EED (chains C, I)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Sequence of entity 3 (D, J), FASTA

>8FYH_3 Histone-binding protein RBBP4 (chains D, J)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 4 (A, G), FASTA

>8FYH_4 Histone-lysine N-methyltransferase EZH2 (chains A, G)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHRKC
NYSFHATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRR
GRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQ
TPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESS
IIAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCP
CVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWD
SKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRG
KVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRA
IQTGEELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 5 (E, K), FASTA

>8FYH_5 protein Jumonji isoform X3 (chains E, K)
MSKERPKRNIIQKKYDDSDGIPWSEERVVRKVLYLSLKEFKNAQKRQHGEGIAGSLKSVN
GLLGNDQSKALGPASEQSENEKDDASQVSSTSNDVSSSDFEEGPSRKRPRLQAQRKFAQS
QPNSPSTTPVKTVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPSSMVYFGSSQ
DEEDVEEEDDETEDVKTANNNASSSCQSTPRKGKTHKHVHNGHVFNGSNRSTREKEPAQK
HKSKETTPAKEKHIDHRADSRREPASVAQPTATPSAGSLAKGLPANHQPPPPHRSAQDLR
KQVTLHVSKVNGVTRMSSLGAGTTSAKKIREVRPSPSKTVKYTATVTKGTVTYTKAKREL
VKETKPTHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASTSTGPAASGLKASSRLNPK
SCTKEVGGRQLREGLRNSKRRLEEAQQVDKPQSPPKKMKGAAGIAEAPGKKASAASAEKS
LLNGHVKKEVPERSLERNRPKRATAGKNMPGKQAHGKAEGTPCENRSTSQPESSHKPHDP
QGKPEKGIGKSGWTAMDEIPVLRPSAKEFHDPLIYIESVRAQVEKYGMCRVIPPPDWRPE
CKLNDEMRFVTQIQHIHKLGRRWGPNVQRLACIKKHLRSQGITMDELPLIGGCELDLACF
FRLINEMGGMQQVTDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQYLLSYDSLSPEEHRR
LEKEVLMEKEILEKRKGPLEGHTENDHHKFHSLPRFEPKNGLIHGVTPRNGFRSKLKEVG
QAPLKTGRRRLFAQEKEVVKEEEEDKGVLNDFHKCIYKGRSVSLTTFYRTARNIMNMCFS
KEPAPAEIEQEYWRLVEEKDCHVAVHCGKVDTNTHGSGFPVGKSEPFSRHGWNLTVLPNN
TGSILRHLGAVPGVTIPWLNIGMVFSTSCWSRDQNHLPYIDYLHTGADCIWYCIPAEEEN
KLEDVVHTLLQANGTPGLQMLESNVMISPEVLCKEGIKVHRTVQQSGQFVVCFPGSFVSK
VCCGYSVSETVHFATTQWTSMGFETAKEMKRRHIAKPFSMEKLLYQIAQAEAKKENGPTL
STISALLDELRDTELRQRRQLFEAGLHSSARYGSHDGNSTVADGKKKPRKWLQLETSERR
CQICQHLCYLSMVVQENENVVFCLECALRHVEKQKSCRGLKLMYRYDEEQIISLVNQICG
KVSGKHGGIENCLNKPTPKRGPRKRATVDVPPSRLPSS

Sequence of entity 6 (F, L), FASTA

>8FYH_6 Zinc finger protein AEBP2 (chains F, L)
MAAAITDMADLEELSRLSPLPPGSPGSAARGRAEPPEEEEEEEEEEEEAEAEAVAALLLN
GGSGGGGGGGGGGVGGGEAETMSEPSPESASQAGEDEDEEEDDEEEEDESSSSGGGEEES
SAESLVGSSGGSSSDETRSLSPGAASSSSGDGDGKEGLEEPKGPRGSQGGGGGGSSSSSV
VSSGGDEGYGTGGGGSSATSGGRRGSLEMSSDGEPLSRMDSEDSISSTIMDVDSTISSGR
STPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHIRSIHVDGQRGGVFVCLWK
GCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQQNSSK
VSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHDFFDAQTLDAIRHRAICFNLSAHIE
SLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDILPDVWVNESERHQLKTKVVHLSKL
PKDTALLLDPNIYRTMPQKRLKRTLIRKVFNLYLSKQ

Sequence of entity 7 (M), FASTA

>8FYH_7 G4 RNA (chains M)
GGGUAAGGGUAAGGGUAAGGGUAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14

Primary citation

Structural basis for inactivation of PRC2 by G-quadruplex RNA. Song, J., Gooding, A.R., Hemphill, W.O. et al. Science (2023) 381:1331-1337. DOI 10.1126/science.adh0059 · 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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