5IJ7: Hs/AcPRC2

Structure of Hs/AcPRC2 in complex with a pyridone inhibitor. Determined by X-ray diffraction at 2.62 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 2.62 Å
Organisms: Anolis carolinensis, Homo sapiens
Chains: 6
Atoms: 15,642
Mol. weight: 275.96 kDa
Ligands: ZN, 6BN
Released: 4 May 2016

Explore 5IJ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IJ7 contains 74 α-helices and 112 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: 24 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	12-61	50
α-helix	65-68	4
β-strand	82-87	6	1
α-helix	91-93	3
β-strand	94-97	4	1
β-strand	99-101	3	2
β-strand	114-115	2	3
β-strand	120-121	2	3
α-helix	168-197	18
α-helix	221-230	10
α-helix	232-234	3
α-helix	237-244	8
α-helix	274-284	11
β-strand	285-286	2	4
β-strand	291-292	2	4
α-helix	300-302	3
α-helix	303-306	4
α-helix	434-443	10
α-helix	451-458	8
α-helix	463-471	9
α-helix	535-538	4
β-strand	543	1	5
β-strand	556	1	5
β-strand	565	1	6
α-helix	572-575	4
β-strand	578	1	7
α-helix	579-581	3
β-strand	601	1	6
α-helix	605-608	4
α-helix	611-613	3
β-strand	614-618	5	8
β-strand	624-628	5	8
β-strand	632	1	9
β-strand	637-640	4	7
β-strand	643-647	5	3
α-helix	648-661	14
β-strand	666-668	3	3
β-strand	673-681	9	3
α-helix	683-686	4
α-helix	687	1
β-strand	688-689	2	7
β-strand	695-702	8	7
β-strand	705-712	8	7
β-strand	716	1	9
α-helix	720	1
β-strand	721	1	8
α-helix	722	1
β-strand	723-724	2	7
α-helix	726-730	5

Chain B: 24 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	12-61	50
α-helix	65-68	4
β-strand	82-87	6	10
α-helix	91-93	3
β-strand	94-97	4	10
β-strand	99-101	3	11
α-helix	102-103	2
β-strand	114-115	2	12
β-strand	120-121	2	12
α-helix	168-196	17
α-helix	221-230	10
α-helix	237-247	11
α-helix	274-284	11
β-strand	285-286	2	13
β-strand	291-292	2	13
α-helix	300-302	3
α-helix	303-306	4
α-helix	434-446	13
α-helix	451-458	8
α-helix	463-471	9
α-helix	535-538	4
β-strand	543	1	14
β-strand	556	1	14
β-strand	565	1	15
α-helix	572-575	4
β-strand	578	1	16
α-helix	579-581	3
β-strand	601	1	15
α-helix	605-608	4
α-helix	611-613	3
β-strand	614-618	5	17
β-strand	624-628	5	17
β-strand	632	1	18
β-strand	637-640	4	16
β-strand	643-647	5	12
α-helix	648-661	14
β-strand	666-668	3	12
β-strand	673-681	9	12
α-helix	683-686	4
α-helix	687	1
β-strand	688-689	2	19
β-strand	695-702	8	16
β-strand	705-712	8	16
β-strand	716	1	18
α-helix	720	1
β-strand	721	1	17
α-helix	722	1
β-strand	723-724	2	19
α-helix	726-730	5

Chain E: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	68-76	9	1
β-strand	82-87	6	2
α-helix	92	1
β-strand	98-103	6	2
β-strand	106-112	7	2
β-strand	118-126	9	2
β-strand	133-140	8	20
β-strand	147-153	7	20
β-strand	158-162	5	20
β-strand	167-172	6	20
β-strand	179-184	6	21
β-strand	191-196	6	21
β-strand	201-205	5	21
β-strand	210-215	6	21
β-strand	225-230	6	22
β-strand	236-241	6	22
β-strand	246-250	5	22
α-helix	254-265	12
α-helix	274-275	2
β-strand	278-280	3	21
β-strand	285-287	3	22
β-strand	297-301	5	23
β-strand	304-308	5	23
β-strand	313-319	7	23
α-helix	326-328	3
β-strand	336-343	8	23
β-strand	355-356	2	24
β-strand	362-366	5	24
β-strand	372-376	5	24
β-strand	387-390	4	24
β-strand	399-404	6	1
β-strand	410-415	6	1
β-strand	419-425	7	1

Chain F: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	68-76	9	10
β-strand	82-87	6	11
α-helix	91-92	2
β-strand	98-103	6	11
β-strand	106-112	7	11
β-strand	118-126	9	11
β-strand	133-140	8	25
β-strand	147-153	7	25
β-strand	158-162	5	25
β-strand	167-172	6	25
β-strand	179-184	6	26
β-strand	191-196	6	26
β-strand	201-205	5	26
β-strand	210-215	6	26
β-strand	225-230	6	27
β-strand	236-241	6	27
β-strand	246-250	5	27
α-helix	254-265	12
α-helix	274-275	2
β-strand	278-280	3	26
β-strand	285-287	3	27
β-strand	297-301	5	28
β-strand	304-308	5	28
β-strand	313-319	7	28
α-helix	326-328	3
β-strand	336-343	8	28
β-strand	355-356	2	29
β-strand	362-366	5	29
β-strand	372-376	5	29
β-strand	387-390	4	29
β-strand	399-404	6	10
β-strand	410-415	6	10
β-strand	419-425	7	10

Chains S and T: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	566	1	8
α-helix	572	1
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	629-631	3
α-helix	632-649	18
α-helix	653-665	13
α-helix	671-686	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2	A, B	protein	643	Anolis carolinensis, Homo sapiens	G1KPH4 (AlphaFold model)
Polycomb protein EED	E, F	protein	362	Homo sapiens	O75530 (AlphaFold model)
Polycomb protein SUZ12	S, T	protein	191	Homo sapiens	Q15022 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IJ7_1 Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2 (chains A, B)
MGQTGKKSEKGPICWRKRVKSEYMRLRQLKRFRRADEVKSMFNSNRQKIQERTEILNQEW
KQRRIQPVHIMTSVSSLRGTRECSVTSDLDFPKQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
LDRRDEKQKNQESNQIDKESHPPRKFPSDKIFEAISSMFPDKGTAEELKEKYKELTEQQL
PGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFHATPNTYKRKNTE
MAIDNKPCGPHCYQHLEGAKEFAAALTAENVEWSGAEASMFRVLIGTYYDNFCAIARLIG
TKTCRQVYEFRVKESSIIAPAPAEDVDTLGGGGSGGGGSGGGGSAAADGSSNHVYNYQPC
DHPRQPCDNSCPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPD
LCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCG
EIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVN
GDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 2 (E, F), FASTA

>5IJ7_2 Polycomb protein EED (chains E, F)
MSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYV
DADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFH
PRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHS
LKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLI
LSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLAL
GNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDR
LR

Sequence of entity 3 (S, T), FASTA

>5IJ7_3 Polycomb protein SUZ12 (chains S, T)
MDYKDDDDKGESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDDEDEKDPEWLRE
KTITQIEEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCR
NFMLHLVSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSE
INSKEKALETD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14
6BN	5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[…	C26 H31 Cl2 N3 O5	2

Primary citation

Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance. Brooun, A., Gajiwala, K.S., Deng, Y.L. et al. Nat Commun (2016) 7:11384-11384. DOI 10.1038/ncomms11384 · PubMed

Other PDB entries of the same protein (UniProt G1KPH4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4W2R 2.81 Å, Structure of Hs/AcPRC2 in complex with 5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihy…
5IJ8 2.99 Å, Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in complex with a pyridone…
6B3W 3.05 Å, Structure of Hs/AcPRC2 in complex with 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(…

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