7KSR: PRC2:EZH1_A from a dimeric PRC2

PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome. Determined by electron microscopy at 4.1 Å resolution. Released 3 Feb 2021.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,863
Mol. weight: 267.01 kDa
Ligands: ZN
Released: 3 Feb 2021

Explore 7KSR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KSR contains 33 α-helices and 104 β-strands across 4 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: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	35-62	28
α-helix	66-68	3
α-helix	70-72	3
β-strand	82-85	4	1
β-strand	95-98	4	1
β-strand	100	1	2
β-strand	115-116	2	3
β-strand	121-122	2	4
α-helix	287-290	4
α-helix	292-297	6
β-strand	298	1	5
β-strand	305	1	5
α-helix	436-449	14
α-helix	453-460	8
α-helix	465-473	9
α-helix	536-540	5
β-strand	544	1	6
β-strand	557	1	6
α-helix	573-576	4
β-strand	579	1	7
α-helix	606-609	4
β-strand	615-619	5	8
β-strand	625-629	5	8
β-strand	638-640	3	7
β-strand	645-647	3	4
α-helix	649-658	10
β-strand	667-668	2	4
β-strand	675-677	3	4
β-strand	681-682	2	3
α-helix	684-687	4
β-strand	689	1	9
β-strand	696-703	8	7
β-strand	706-713	8	7
β-strand	722	1	8
β-strand	724	1	9

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	83-89	7	27
β-strand	90	1	1
β-strand	98-101	4	2
α-helix	110-111	2
β-strand	112-116	5	2
β-strand	121-125	5	2
β-strand	134-138	5	2
β-strand	147-154	8	28
β-strand	161-167	7	28
β-strand	171-176	6	28
β-strand	181-187	7	28
β-strand	193-198	6	29
β-strand	205-210	6	29
β-strand	215-219	5	29
β-strand	224-228	5	29
β-strand	239-244	6	30
β-strand	251-255	5	30
β-strand	260-262	3	30
α-helix	268-278	11
β-strand	292-293	2	29
β-strand	299	1	30
β-strand	312-315	4	31
β-strand	318-321	4	31
β-strand	327-333	7	31
α-helix	340-342	3
β-strand	350-357	8	31
β-strand	368-369	2	32
β-strand	376-379	4	32
β-strand	386-390	5	32
α-helix	396-398	3
β-strand	401-404	4	32
β-strand	416-418	3	27
β-strand	424-428	5	27
β-strand	433-438	6	27

Chain C: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	80-106	27
α-helix	112-114	3
α-helix	137-144	8
β-strand	156	1	18
β-strand	160-161	2	19
β-strand	164	1	20
β-strand	185-191	7	21
α-helix	201-202	2
β-strand	203-210	8	21
β-strand	215	1	20
β-strand	234	1	18
β-strand	247-253	7	21
β-strand	296-299	4	21
β-strand	302	1	22
β-strand	308	1	22
β-strand	314-317	4	19
β-strand	355-358	4	19
β-strand	429-430	2	23
β-strand	431-434	4	24
β-strand	437-441	5	24
α-helix	460-469	10
β-strand	474	1	25
β-strand	477-479	3	23
β-strand	486-488	3	23
β-strand	491	1	25
β-strand	525-530	6	10
β-strand	566	1	26
α-helix	572	1
β-strand	573	1	26
α-helix	574-575	2
α-helix	590-601	12
α-helix	608-623	16
α-helix	632-648	17
α-helix	653-665	13
α-helix	671-685	15

Chain D: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
α-helix	28-30	3
β-strand	32-39	8	10
β-strand	47-54	8	11
β-strand	61-68	8	11
β-strand	77-87	11	11
β-strand	115-123	9	11
β-strand	130-132	3	12
β-strand	139-142	4	12
β-strand	149-153	5	12
β-strand	171-173	3	12
β-strand	183-185	3	13
β-strand	192-197	6	13
β-strand	201-206	6	13
β-strand	221-223	3	13
β-strand	230-235	6	14
β-strand	242-247	6	14
β-strand	251-256	6	14
β-strand	267-269	3	14
β-strand	276-281	6	15
β-strand	288-293	6	15
β-strand	297-302	6	15
β-strand	311-313	3	15
β-strand	320-322	3	16
β-strand	332-335	4	17
β-strand	336-337	2	16
β-strand	342-346	5	17
α-helix	356-361	6
β-strand	366-370	5	17
β-strand	377-382	6	10
β-strand	389-394	6	10
β-strand	399-404	6	10
α-helix	406-409	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase EZH1	A	protein	747	Homo sapiens	Q92800 (AlphaFold model)
Histone-binding protein RBBP4	D	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Polycomb protein SUZ12	C	protein	739	Homo sapiens	Q15022 (AlphaFold model)
Polycomb protein EED	B	protein	441	Homo sapiens	O75530 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7KSR_1 Histone-lysine N-methyltransferase EZH1 (chains A)
MEIPNPPTSKCITYWKRKVKSEYMRLRQLKRLQANMGAKALYVANFAKVQEKTQILNEEW
KKLRVQPVQSMKPVSGHPFLKKCTIESIFPGFASQHMLMRSLNTVALVPIMYSWSPLQQN
FMVEDETVLCNIPYMGDEVKEEDETFIEELINNYDGKVHGEEEMIPGSVLISDAVFLELV
DALNQYSDEEEEGHNDTSDGKQDDSKEDLPVTRKRKRHAIEGNKKSSKKQFPNDMIFSAI
ASMFPENGVPDDMKERYRELTEMSDPNALPPQCTPNIDGPNAKSVQREQSLHSFHTLFCR
RCFKYDCFLHPFHATPNVYKRKNKEIKIEPEPCGTDCFLLLEGAKEYAMLHNPRSKCSGR
RRRRHHIVSASCSNASASAVAETKEGDSDRDTGNDWASSSSEANSRCQTPTKQKASPAPP
QLCVVEAPSEPVEWTGAEESLFRVFHGTYFNNFCSIARLLGTKTCKQVFQFAVKESLILK
LPTDELMNPSQKKKRKHRLWAAHCRKIQLKKDNSSTQVYNYQPCDHPDRPCDSTCPCIMT
QNFCEKFCQCNPDCQNRFPGCRCKTQCNTKQCPCYLAVRECDPDLCLTCGASEHWDCKVV
SCKNCSIQRGLKKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYD
KYMSSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVVMVNGDHRIGIFAKRAIQAG
EELFFDYRYSQADALKYVGIERETDVL

Sequence of entity 2 (D), FASTA

>7KSR_2 Histone-binding protein RBBP4 (chains D)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 3 (C), FASTA

>7KSR_3 Polycomb protein SUZ12 (chains C)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL

Sequence of entity 4 (B), FASTA

>7KSR_4 Polycomb protein EED (chains B)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

Primary citation

Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction. Grau, D., Zhang, Y., Lee, C.H. et al. Nat Commun (2021) 12:714-714. DOI 10.1038/s41467-020-20775-z · PubMed

Other PDB entries of the same protein (UniProt Q92800 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TD5 2.99 Å, Structure of human PRC2-EZH1 containing phosphorylated SUZ12
7KSO 3.9 Å, Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2
7KTP 4.8 Å, PRC2:EZH1_B from a dimeric PRC2 bound to a nucleosome

Browse structure collections

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