9XZI: SUZ12-RBBP4-PHF19-EPOP PRC2.1 Subcomplex

Crystal Structure of the SUZ12-RBBP4-PHF19-EPOP PRC2.1 Subcomplex. Determined by X-ray diffraction at 2.69 Å resolution. Released 11 Feb 2026.

Method: X-ray diffraction
Resolution: 2.69 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,163
Mol. weight: 119.11 kDa
Ligands: ZN
Released: 11 Feb 2026

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

Secondary structure: helices and β-sheets

9XZI contains 20 α-helices and 52 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	84-87	4
α-helix	91-104	14
α-helix	112-114	3
α-helix	119-121	3
α-helix	134-136	3
α-helix	137-142	6
β-strand	157-165	9	1
β-strand	181-192	12	2
α-helix	193-195	3
β-strand	203-214	12	2
β-strand	215	1	1
β-strand	229-232	4	1
α-helix	234-236	3
β-strand	245-255	11	2
β-strand	295-302	8	2
β-strand	308	1	2
β-strand	313-318	6	1
β-strand	320-321	2	2
β-strand	332-335	4	1
α-helix	347-351	5
β-strand	354-361	8	1
β-strand	429-433	5	3
β-strand	440-444	5	3
β-strand	449	1	4
β-strand	456	1	4
α-helix	460-470	11
β-strand	474-480	7	3
β-strand	485-491	7	3
β-strand	525-531	7	5

Chain B: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	6-27	22
α-helix	28-30	3
β-strand	32-39	8	5
β-strand	47-54	8	6
β-strand	61-69	9	6
β-strand	77-87	11	6
β-strand	115-123	9	6
β-strand	129-133	5	7
β-strand	136-143	8	7
α-helix	148	1
β-strand	149-153	5	7
α-helix	154-156	3
α-helix	161-162	2
β-strand	171-174	4	7
β-strand	183-185	3	8
β-strand	192-196	5	8
β-strand	202-206	5	8
β-strand	216-218	3	7
β-strand	221-223	3	8
β-strand	230-235	6	9
β-strand	242-247	6	9
β-strand	251-256	6	9
β-strand	267-270	4	9
β-strand	276-281	6	10
β-strand	288-293	6	10
β-strand	297-302	6	10
β-strand	311-314	4	10
β-strand	320-325	6	11
β-strand	332-337	6	11
β-strand	342-346	5	11
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	11
β-strand	377-382	6	5
β-strand	389-394	6	5
β-strand	398-404	7	5

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	544-550	7
β-strand	555-562	8	1
β-strand	568-574	7	1
α-helix	577-578	2

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	316-318	3
β-strand	325-327	3	12
β-strand	333-335	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polycomb protein SUZ12	A	protein	473	Homo sapiens	Q15022 (AlphaFold model)
Histone-binding protein RBBP4	B	protein	444	Homo sapiens	Q09028 (AlphaFold model)
PHD finger protein 19	C	protein	53	Homo sapiens	Q5T6S3 (AlphaFold model)
Elongin BC and Polycomb repressive complex 2-associated protein	D	protein	78	Homo sapiens	A6NHQ4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9XZI_1 Polycomb protein SUZ12 (chains A)
SNAMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTF
KVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVC
HKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLF
RVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLD
GEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAP
IAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQF
LYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSIN
ECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLE

Sequence of entity 2 (B), FASTA

>9XZI_2 Histone-binding protein RBBP4 (chains B)
MGSSHHHHHHSSGLVPRGSMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALE
WPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSE
KGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKP
DPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKT
IFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSF
NPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRR
LNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQV
WQMAENIYNDEDPEGSVDPEGQGS

Sequence of entity 3 (C), FASTA

>9XZI_3 PHD finger protein 19 (chains C)
SNASLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLVEWEGTTPY

Sequence of entity 4 (D), FASTA

>9XZI_4 Elongin BC and Polycomb repressive complex 2-associated protein (chains D)
SSTFSLLNCFPCPPALVVGEDGDLKPASSLRLQGDSKPPPAHPLWRWQMGGPAVPEPPGL
KFWGINMDESDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

EPOP restricts PRC2.1 targeting to chromatin by directly modulating enzyme complex dimerization. Gong, L., Liu, X., Yang, X. et al. Nat Commun (2026) 17:1565-1565. DOI 10.1038/s41467-025-68280-5 · 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
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
9C8U 3.1 Å, Human PRC2 - RvLEAM (short) (1:6 molar ratio), cross-linked 10 min

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