7TD5: Human PRC2-EZH1 containing phosphorylated SUZ12

Structure of human PRC2-EZH1 containing phosphorylated SUZ12. Determined by X-ray diffraction at 2.99 Å resolution. Released 16 Nov 2022.

Method: X-ray diffraction
Resolution: 2.99 Å
Organism: Homo sapiens
Chains: 10
Atoms: 16,191
Mol. weight: 304.79 kDa
Ligands: ZN, SAM
Released: 16 Nov 2022

Explore 7TD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TD5 contains 74 α-helices and 123 β-strands across 10 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: 25 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	24-62	39
β-strand	65	1	1
α-helix	66-68	3
β-strand	81-87	7	2
β-strand	95-99	5	2
β-strand	100-102	3	3
α-helix	103-104	2
α-helix	107-110	4
β-strand	115-116	2	4
β-strand	121-122	2	4
α-helix	124-126	3
β-strand	129	1	5
α-helix	132-134	3
α-helix	141-154	14
β-strand	158	1	5
α-helix	274-276	3
α-helix	287-290	4
α-helix	292-297	6
β-strand	298-299	2	6
β-strand	304-305	2	6
α-helix	316-319	4
α-helix	338-340	3
β-strand	342	1	7
α-helix	344-351	8
β-strand	426	1	7
α-helix	436-449	14
α-helix	453-460	8
α-helix	465-476	12
α-helix	536-539	4
β-strand	544	1	8
β-strand	557	1	8
α-helix	573-576	4
β-strand	579	1	9
α-helix	580-582	3
β-strand	615-619	5	10
β-strand	625-629	5	10
β-strand	633	1	11
β-strand	638-641	4	9
β-strand	644-647	4	4
α-helix	649-661	13
β-strand	667-669	3	4
β-strand	675-682	8	4
α-helix	684-687	4
α-helix	688	1
β-strand	689-690	2	9
β-strand	696-702	7	9
β-strand	707-713	7	9
β-strand	717	1	11
α-helix	721	1
β-strand	722	1	10
α-helix	723	1
β-strand	724-725	2	9
α-helix	731-737	7

Chain B: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	77-78	2
β-strand	82-90	9	2
β-strand	96-101	6	3
β-strand	105	1	1
α-helix	106	1
α-helix	110	1
β-strand	111-117	7	3
β-strand	120-126	7	3
β-strand	132-140	9	3
β-strand	147-154	8	12
β-strand	161-167	7	12
β-strand	171-176	6	12
β-strand	181-187	7	12
β-strand	193-198	6	13
β-strand	205-210	6	13
β-strand	215-219	5	13
β-strand	224-229	6	13
β-strand	239-244	6	14
β-strand	250-255	6	14
β-strand	260-264	5	14
α-helix	268-279	12
α-helix	288-289	2
β-strand	292-294	3	13
β-strand	299-301	3	14
β-strand	311-315	5	15
β-strand	318-322	5	15
β-strand	327-333	7	15
α-helix	340-342	3
β-strand	350-357	8	15
β-strand	367	1	2
β-strand	369-370	2	16
β-strand	376-380	5	16
β-strand	386-390	5	16
α-helix	396-398	3
β-strand	400-404	5	16
β-strand	406	1	17
β-strand	409	1	17
β-strand	413-418	6	2
β-strand	424-429	6	2
β-strand	433-439	7	2
α-helix	440	1

Chain C: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	566	1	10
β-strand	573	1	10
α-helix	576-578	3
α-helix	590-602	13
α-helix	608-624	17
α-helix	631-649	19
α-helix	653-665	13
α-helix	671-691	21

Chains D and I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	27	1	4

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3

Chain F: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	24-62	39
α-helix	65-68	4
β-strand	82-87	6	18
β-strand	95-98	4	18
β-strand	100-102	3	19
α-helix	106-110	5
β-strand	115-116	2	20
β-strand	121-122	2	21
α-helix	124-126	3
β-strand	129	1	22
α-helix	132-134	3
α-helix	141-154	14
β-strand	158	1	22
α-helix	287-297	11
β-strand	298-299	2	23
β-strand	304-305	2	23
α-helix	436-446	11
α-helix	453-460	8
α-helix	465-474	10
α-helix	536-539	4
α-helix	573-576	4
β-strand	579	1	24
α-helix	580-582	3
β-strand	615-619	5	25
β-strand	625-629	5	25
β-strand	633	1	26
β-strand	638-641	4	24
β-strand	645-647	3	21
α-helix	649-661	13
β-strand	667-669	3	21
β-strand	675-677	3	21
β-strand	681-682	2	20
α-helix	684-687	4
α-helix	688	1
β-strand	689-690	2	24
β-strand	696-702	7	24
β-strand	707-713	7	24
β-strand	717	1	26
α-helix	721	1
β-strand	722	1	25
α-helix	723	1
β-strand	724-725	2	24
α-helix	731-737	7

Chain G: 7 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	77-78	2
β-strand	82-90	9	18
β-strand	96-101	6	19
α-helix	106	1
α-helix	110	1
β-strand	111-117	7	19
β-strand	120-126	7	19
α-helix	128-130	3
β-strand	132-140	9	19
β-strand	147-154	8	27
β-strand	161-167	7	27
β-strand	171-176	6	27
β-strand	181-187	7	27
β-strand	193-198	6	28
β-strand	205-210	6	28
β-strand	215-219	5	28
β-strand	224-229	6	28
β-strand	239-244	6	29
β-strand	250-255	6	29
β-strand	260-264	5	29
α-helix	268-279	12
β-strand	292-294	3	28
β-strand	299-301	3	29
β-strand	311-315	5	30
β-strand	318-322	5	30
β-strand	327-333	7	30
α-helix	340-342	3
β-strand	350-357	8	30
β-strand	363	1	31
β-strand	367	1	18
β-strand	369-370	2	32
β-strand	376-380	5	32
β-strand	386-390	5	32
α-helix	396-398	3
β-strand	400-404	5	32
β-strand	413-418	6	18
β-strand	424-429	6	18
β-strand	433-439	7	18

Chain H: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	566	1	25
β-strand	573	1	25
α-helix	576-578	3
α-helix	590-601	12
α-helix	608-624	17
α-helix	629-631	3
α-helix	632-649	18
α-helix	653-665	13
α-helix	671-691	21

1 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
Histone-lysine N-methyltransferase EZH1	A, F	protein	747	Homo sapiens	Q92800 (AlphaFold model)
Polycomb protein EED	B, G	protein	373	Homo sapiens	O75530 (AlphaFold model)
Polycomb protein SUZ12	C, H	protein	179	Homo sapiens	Q15022 (AlphaFold model)
Thr-lys-ala-ala-arg-met-ser-ala-pro-ser	D, I	protein	10	Homo sapiens	P68431 (AlphaFold model)
Thr-lys-ala-ala-arg-M3L-ser-ala-pro-ala	E, J	protein	10	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>7TD5_1 Histone-lysine N-methyltransferase EZH1 (chains A, F)
MEIPNPPTSKCITYWKRKVKSEYMRLRQLKRLQANMGAKALYVANFAKVQEKTQILNEEW
KKLRVQPVQSMKPVSGHPFLKKCTIESIFPGFASQHMLMRSLNTVALVPIMYSWSPLQQN
FMVEDETVLCNIPYMGDEVKEEDETFIEELINNYDGKVHGEEEMIPGSVLISDAVFLELV
DALNQYSDEEEEGHNDTSDGKQDDSKEDLPVTRKRKRHAIEGNKKSSKKQFPNDMIFSAI
ASMFPENGVPDDMKERYRELTEMSDPNALPPQCTPNIDGPNAKSVQREQSLHSFHTLFCR
RCFKYDCFLHPFHATPNVYKRKNKEIKIEPEPCGTDCFLLLEGAKEYAMLHNPRSKCSGR
RRRRHHIVSASCSNASASAVAETKEGDSDRDTGNDWASSSSEANSRCQTPTKQKASPAPP
QLCVVEAPSEPVEWTGAEESLFRVFHGTYFNNFCSIARLLGTKTCKQVFQFAVKESLILK
LPTDELMNPSQKKKRKHRLWAAHCRKIQLKKDNSSTQVYNYQPCDHPDRPCDSTCPCIMT
QNFCEKFCQCNPDCQNRFPGCRCKTQCNTKQCPCYLAVRECDPDLCLTCGASEHWDCKVV
SCKNCSIQRGLKKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYD
KYMSSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVVMVNGDHRIGIFAKRAIQAG
EELFFDYRYSQADALKYVGIERETDVL

Sequence of entity 2 (B, G), FASTA

>7TD5_2 Polycomb protein EED (chains B, G)
SWSHPQFEKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHS
QGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVG
HGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLG
EKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNY
VDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRF
SMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAV
CDDASIWRWDRLR

Sequence of entity 3 (C, H), FASTA

>7TD5_3 Polycomb protein SUZ12 (chains C, H)
HNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDVNEGEKEVMKLWNLH
VMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSIDKAVTK
LREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEKALETDSVSGVSKQSKKQKL

Sequence of entity 4 (D, I), FASTA

>7TD5_4 THR-LYS-ALA-ALA-ARG-MET-SER-ALA-PRO-SER (chains D, I)
TKAARMSAPS

Sequence of entity 5 (E, J), FASTA

>7TD5_5 THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA (chains E, J)
TKAARKSAPA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	16
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	2

Primary citation

CK2-mediated phosphorylation of SUZ12 promotes PRC2 function by stabilizing enzyme active site. Gong, L., Liu, X., Jiao, L. et al. Nat Commun (2022) 13:6781-6781. DOI 10.1038/s41467-022-34431-1 · PubMed

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

7KSO 3.9 Å, Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2
7KSR 4.1 Å, PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome
7KTP 4.8 Å, PRC2:EZH1_B from a dimeric PRC2 bound to a nucleosome

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