9C8U: Polycomb protein SUZ12

Human PRC2 - RvLEAM (short) (1:6 molar ratio), cross-linked 10 min. Determined by electron microscopy at 3.1 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 12,252
Mol. weight: 296.07 kDa
Ligands: ZN
Released: 4 Sept 2024

Explore 9C8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C8U contains 53 α-helices and 109 β-strands across 6 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: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	23-60	38
α-helix	66-68	3
β-strand	82-85	4	23
β-strand	94-97	4	23
α-helix	98	1
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	274-277	4
α-helix	279-283	5
β-strand	285-286	2	26
β-strand	291-292	2	26
α-helix	304-306	3
α-helix	336-344	9
α-helix	430-433	4
α-helix	439-452	14
α-helix	456-462	7
α-helix	468-478	11
α-helix	540-543	4
α-helix	562-565	4
β-strand	570	1	27
α-helix	577-580	4
β-strand	583	1	28
β-strand	606	1	27
α-helix	610-613	4
β-strand	619-623	5	7
β-strand	629-633	5	7
β-strand	637	1	29
β-strand	642-645	4	28
β-strand	649-651	3	25
α-helix	653-663	11
β-strand	671-673	3	25
β-strand	679-681	3	25
β-strand	685-686	2	24
α-helix	688-690	3
β-strand	693	1	30
β-strand	700-707	8	28
β-strand	710-717	8	28
β-strand	721	1	29
α-helix	725	1
β-strand	726	1	7
α-helix	727	1
β-strand	728	1	30
β-strand	729	1	28
α-helix	738-741	4

Chain B: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	81-103	23
α-helix	112-114	3
α-helix	135-139	5
α-helix	140-144	5
β-strand	185-192	8	1
α-helix	193-194	2
β-strand	203-206	4	1
β-strand	245-253	9	1
β-strand	296-300	5	1
β-strand	316	1	2
β-strand	428-432	5	3
β-strand	434	1	4
β-strand	438	1	4
β-strand	441-443	3	3
β-strand	449	1	5
β-strand	456	1	5
α-helix	460-470	11
β-strand	474-478	5	3
β-strand	485-491	7	3
α-helix	503-507	5
α-helix	509	1
β-strand	525-530	6	6
α-helix	540-543	4
β-strand	557-560	4	6
β-strand	566	1	7
β-strand	573	1	7
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: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	8
β-strand	96-101	6	9
α-helix	106	1
β-strand	111-117	7	9
β-strand	120-126	7	9
α-helix	128-130	3
β-strand	132-137	6	9
β-strand	138-139	2	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	239-244	6	13
β-strand	250-255	6	13
β-strand	260-264	5	13
α-helix	268-278	11
β-strand	292-293	2	12
β-strand	300-301	2	13
β-strand	309-315	7	14
β-strand	318-323	6	14
β-strand	327-333	7	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	413-418	6	8
β-strand	424-429	6	8
β-strand	434-439	6	8

Chain D: 8 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	4-26	23
α-helix	28-30	3
β-strand	32-39	8	6
β-strand	47-54	8	16
β-strand	62-68	7	16
β-strand	77-78	2	17
β-strand	81-86	6	16
β-strand	117-119	3	16
β-strand	122-123	2	17
α-helix	131	1
β-strand	132	1	18
α-helix	133	1
β-strand	139-143	5	18
β-strand	149-153	5	18
α-helix	161-162	2
β-strand	172-173	2	18
β-strand	180-185	6	19
β-strand	193-197	5	19
β-strand	202-205	4	19
β-strand	216-217	2	18
β-strand	221-223	3	19
β-strand	230-235	6	20
β-strand	242-247	6	20
β-strand	251-256	6	20
β-strand	267-269	3	20
β-strand	276-281	6	21
β-strand	288-293	6	21
β-strand	298-302	5	21
β-strand	305	1	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	6
β-strand	390-394	5	6
β-strand	398-404	7	6
α-helix	406-409	4

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	142	1	3
α-helix	143-148	6

Chain F: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	183-185	3
α-helix	193-209	17
β-strand	219-223	5	31
β-strand	239-241	3	2
β-strand	252-254	3	2
α-helix	256-261	6
β-strand	264-268	5	31
α-helix	277-280	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polycomb protein SUZ12	B	protein	739	Homo sapiens	Q15022 (AlphaFold model)
Polycomb protein EED	C	protein	367	Homo sapiens	O75530 (AlphaFold model)
RBAP48	D	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Isoform 2 of Histone-lysine N-methyltransferase EZH2	A	protein	750	Homo sapiens	Q15910 (AlphaFold model)
Protein Jumonji	E	protein	31	Homo sapiens	Q92833
Zinc finger protein AEBP2	F	protein	294	Homo sapiens	Q6ZN18

Sequence of entity 1 (B), FASTA

>9C8U_1 Polycomb protein SUZ12 (chains B)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL

Sequence of entity 2 (C), FASTA

>9C8U_2 Polycomb protein EED (chains C)
SKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRL
LQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAIN
ELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSC
GMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRW
LGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQ
KMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASI
WRWDRLR

Sequence of entity 3 (D), FASTA

>9C8U_3 RBAP48 (chains D)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 4 (A), FASTA

>9C8U_4 Isoform 2 of Histone-lysine N-methyltransferase EZH2 (chains A)
GQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEWK
QRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNFM
VEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQY
NDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEELK
EKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHRKCN
YSFHATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRG
RLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQT
PIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSI
IAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPC
VIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDS
KNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGK
VYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAI
QTGEELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 5 (E), FASTA

>9C8U_5 Protein Jumonji (chains E)
PPATQISDLSKRKPKTEDFLTFLCLRGSPAL

Sequence of entity 6 (F), FASTA

>9C8U_6 Zinc finger protein AEBP2 (chains F)
SSDGEPLSRMDSEDSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQ
ACFNSSPDLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFK
CVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRR
SLPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLL
HWMPEDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

Primary citation

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing. Abe, K.M., Li, G., He, Q. et al. Nat Commun (2024) 15:7705-7705. DOI 10.1038/s41467-024-52091-1 · 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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