8VNV: PRC2_AJ1-450
PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged. Determined by electron microscopy at 3.1 Å resolution. Released 22 Jan 2025.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Homo sapiens
- Chains
- 9
- Atoms
- 15,927
- Mol. weight
- 353.99 kDa
- Ligands
- SAH
- Released
- 22 Jan 2025
Explore 8VNV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8VNV contains 74 α-helices and 116 β-strands across 7 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: 17 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 84-106 | 23 | |
| α-helix | 112-114 | 3 | |
| α-helix | 116-118 | 3 | |
| α-helix | 132-134 | 3 | |
| α-helix | 135-145 | 11 | |
| β-strand | 157-161 | 5 | 1 |
| α-helix | 162-164 | 3 | |
| β-strand | 165 | 1 | 1 |
| β-strand | 184-192 | 9 | 2 |
| β-strand | 203-211 | 9 | 2 |
| β-strand | 230-232 | 3 | 1 |
| α-helix | 239-242 | 4 | |
| β-strand | 245-253 | 9 | 2 |
| β-strand | 296-300 | 5 | 2 |
| β-strand | 302 | 1 | 3 |
| β-strand | 308 | 1 | 3 |
| β-strand | 313-318 | 6 | 1 |
| β-strand | 320 | 1 | 2 |
| β-strand | 354-361 | 8 | 1 |
| β-strand | 427-434 | 8 | 4 |
| β-strand | 438-444 | 7 | 4 |
| β-strand | 449 | 1 | 5 |
| β-strand | 456 | 1 | 5 |
| α-helix | 460-469 | 10 | |
| β-strand | 474-478 | 5 | 4 |
| β-strand | 484-491 | 8 | 4 |
| α-helix | 504-507 | 4 | |
| α-helix | 509 | 1 | |
| β-strand | 525-530 | 6 | 6 |
| α-helix | 540-542 | 3 | |
| β-strand | 557-560 | 4 | 6 |
| β-strand | 566 | 1 | 7 |
| β-strand | 573 | 1 | 7 |
| α-helix | 577-579 | 3 | |
| α-helix | 590-601 | 12 | |
| α-helix | 608-622 | 15 | |
| α-helix | 631-650 | 20 | |
| α-helix | 653-664 | 12 | |
| α-helix | 671-681 | 11 | |
Chain B: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 145-150 | 6 | |
| α-helix | 162-165 | 4 | |
Chain C: 31 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-61 | 43 | |
| α-helix | 66-68 | 3 | |
| β-strand | 82-85 | 4 | 22 |
| β-strand | 86-87 | 2 | 8 |
| α-helix | 92-93 | 2 | |
| β-strand | 94-97 | 4 | 22 |
| α-helix | 98 | 1 | |
| β-strand | 99-100 | 2 | 9 |
| α-helix | 101-103 | 3 | |
| β-strand | 114-115 | 2 | 23 |
| β-strand | 120-121 | 2 | 24 |
| β-strand | 128 | 1 | 25 |
| α-helix | 131-133 | 3 | |
| α-helix | 138-140 | 3 | |
| α-helix | 144-152 | 9 | |
| β-strand | 157 | 1 | 25 |
| α-helix | 170-177 | 8 | |
| α-helix | 222-230 | 9 | |
| α-helix | 237-249 | 13 | |
| α-helix | 274-277 | 4 | |
| α-helix | 279-284 | 6 | |
| β-strand | 285-286 | 2 | 26 |
| β-strand | 291-292 | 2 | 26 |
| α-helix | 329-337 | 9 | |
| α-helix | 434-447 | 14 | |
| α-helix | 451-456 | 6 | |
| α-helix | 463-473 | 11 | |
| α-helix | 474-476 | 3 | |
| α-helix | 478-480 | 3 | |
| α-helix | 495-509 | 15 | |
| α-helix | 510-513 | 4 | |
| α-helix | 517-520 | 4 | |
| α-helix | 535-538 | 4 | |
| β-strand | 543 | 1 | 27 |
| β-strand | 556 | 1 | 27 |
| α-helix | 572-575 | 4 | |
| β-strand | 578 | 1 | 28 |
| α-helix | 605-608 | 4 | |
| β-strand | 614-618 | 5 | 7 |
| β-strand | 624-628 | 5 | 7 |
| β-strand | 632 | 1 | 29 |
| β-strand | 637-640 | 4 | 28 |
| β-strand | 644-647 | 4 | 24 |
| α-helix | 648-661 | 14 | |
| β-strand | 666-668 | 3 | 24 |
| β-strand | 673-676 | 4 | 24 |
| β-strand | 680-681 | 2 | 23 |
| α-helix | 683-686 | 4 | |
| α-helix | 687 | 1 | |
| β-strand | 688 | 1 | 30 |
| α-helix | 689 | 1 | |
| β-strand | 695-702 | 8 | 28 |
| β-strand | 705-712 | 8 | 28 |
| β-strand | 716 | 1 | 29 |
| β-strand | 720-721 | 2 | 7 |
| α-helix | 722 | 1 | |
| β-strand | 723 | 1 | 30 |
| α-helix | 730-736 | 7 | |
Chain I: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27 | 1 | 24 |
| α-helix | 36-39 | 4 | |
Chain L: 6 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 82-89 | 8 | 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 | 132-139 | 8 | 9 |
| β-strand | 147 | 1 | 10 |
| β-strand | 151-154 | 4 | 11 |
| β-strand | 161-166 | 6 | 11 |
| β-strand | 167 | 1 | 10 |
| 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 | 214-219 | 6 | 12 |
| β-strand | 225 | 1 | 12 |
| β-strand | 228-230 | 3 | 12 |
| β-strand | 239-244 | 6 | 13 |
| β-strand | 250-255 | 6 | 13 |
| β-strand | 260-264 | 5 | 13 |
| α-helix | 268-278 | 11 | |
| α-helix | 288-289 | 2 | |
| β-strand | 293-294 | 2 | 12 |
| β-strand | 299-301 | 3 | 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 | 368-370 | 3 | 15 |
| β-strand | 376-379 | 4 | 15 |
| β-strand | 386-390 | 5 | 15 |
| α-helix | 396-398 | 3 | |
| β-strand | 403-404 | 2 | 15 |
| α-helix | 412 | 1 | |
| β-strand | 413-418 | 6 | 8 |
| β-strand | 424-429 | 6 | 8 |
| β-strand | 433-439 | 7 | 8 |
Chain N: 10 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-27 | 22 | |
| α-helix | 28-30 | 3 | |
| β-strand | 32-39 | 8 | 6 |
| β-strand | 48-54 | 7 | 16 |
| β-strand | 61-67 | 7 | 16 |
| β-strand | 78-87 | 10 | 16 |
| β-strand | 115-122 | 8 | 16 |
| β-strand | 129-132 | 4 | 17 |
| β-strand | 139-143 | 5 | 17 |
| β-strand | 149-153 | 5 | 17 |
| α-helix | 154-156 | 3 | |
| α-helix | 161-162 | 2 | |
| α-helix | 167-169 | 3 | |
| β-strand | 171-173 | 3 | 17 |
| β-strand | 182-185 | 4 | 18 |
| β-strand | 192-196 | 5 | 18 |
| β-strand | 202-206 | 5 | 18 |
| α-helix | 211-213 | 3 | |
| β-strand | 216-217 | 2 | 17 |
| β-strand | 221-223 | 3 | 18 |
| β-strand | 230-235 | 6 | 19 |
| β-strand | 242-247 | 6 | 19 |
| β-strand | 251-256 | 6 | 19 |
| β-strand | 269-270 | 2 | 19 |
| β-strand | 276-281 | 6 | 20 |
| β-strand | 288-293 | 6 | 20 |
| β-strand | 298-302 | 5 | 20 |
| β-strand | 305-313 | 9 | 20 |
| β-strand | 320-325 | 6 | 21 |
| α-helix | 326 | 1 | |
| β-strand | 332-337 | 6 | 21 |
| β-strand | 342-346 | 5 | 21 |
| α-helix | 347-349 | 3 | |
| α-helix | 356-361 | 6 | |
| β-strand | 366-370 | 5 | 21 |
| β-strand | 377-382 | 6 | 6 |
| β-strand | 389-394 | 6 | 6 |
| β-strand | 398-404 | 7 | 6 |
| α-helix | 406-408 | 3 | |
Chain P: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 183-185 | 3 | |
| α-helix | 192-209 | 18 | |
| α-helix | 211-215 | 5 | |
| β-strand | 219-223 | 5 | 31 |
| β-strand | 226-231 | 6 | 1 |
| β-strand | 237-241 | 5 | 1 |
| α-helix | 249-251 | 3 | |
| β-strand | 253-255 | 3 | 1 |
| α-helix | 256-258 | 3 | |
| β-strand | 264-268 | 5 | 31 |
| α-helix | 269-271 | 3 | |
| α-helix | 278-280 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Polycomb protein SUZ12 | A | protein | 619 | Homo sapiens | Q15022 (AlphaFold model) |
| EED | L | protein | 441 | Homo sapiens | O75530 (AlphaFold model) |
| RBAP48 | N | protein | 425 | Homo sapiens | Q09028 (AlphaFold model) |
| Isoform 2 of Histone-lysine N-methyltransferase EZH2 | C | protein | 746 | Homo sapiens | Q15910 (AlphaFold model) |
| Protein Jumonji | B | protein | 449 | Homo sapiens | Q92833 |
| Zinc finger protein AEBP2 | P | protein | 279 | Homo sapiens | Q6ZN18 |
| DNA (26-mer) | H | DNA | 23 | Homo sapiens | |
| H3K36me3-modified histone H3 | I | protein | 22 | Homo sapiens | P68431 |
| DNA (26-mer) | D | DNA | 26 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>8VNV_1 Polycomb protein SUZ12 (chains A)
MVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTN
IKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEV
LLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVK
SYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNR
RLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETN
DKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTNLQTRKEKDTPNENRQKL
RIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGAR
IDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLES
EDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDV
NEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDF
NLISIMSIDKAVTKLREMQ
Sequence of entity 2 (L), FASTA
>8VNV_2 EED (chains L)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR
Sequence of entity 3 (N), FASTA
>8VNV_3 RBAP48 (chains N)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS
Sequence of entity 4 (C), FASTA
>8VNV_4 Isoform 2 of Histone-lysine N-methyltransferase EZH2 (chains C)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH
ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPN
NSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKM
KPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA
PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQ
NFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS
CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK
YMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE
ELFFDYRYSQADALKYVGIEREMEIP
Sequence of entity 5 (B), FASTA
>8VNV_5 Protein Jumonji (chains B)
SKERPKRNIIQKKYDDSDGIPWSEERVVRKVLYLSLKEFKNSQKRQHAEGIAGSLKTVNG
LLGNDQSKGLGPASEQSENEKDDASQVSSTSNDVSSSDFEEGPSRKRPRLQAQRKFAQSQ
PNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYFGSSQD
EEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKEPVQKH
KSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAATHHHPPLHRSAQDLRK
QVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKRELVKDTK
PNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPKSCTKE
VGGRQLREGLQLREGLRNSKRRLEEAHQA
Sequence of entity 6 (P), FASTA
>8VNV_6 Zinc finger protein AEBP2 (chains P)
ISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHIRS
IHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCNASFASQGG
LARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHDFFDAQTLD
AIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDILPDVWVNE
SERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR
Sequence of entity 7 (H), FASTA
>8VNV_7 DNA (26-mer) (chains H)
GGGATTCTCCAGCCGCCGGCAGC
Sequence of entity 8 (I), FASTA
>8VNV_8 H3K36me3-modified histone H3 (chains I)
QLATKAARKSAPATGGVKKPHR
Sequence of entity 9 (D), FASTA
>8VNV_9 DNA (26-MER) (chains D)
GCTGCCGGCGGCTGGAGAATCCCGGT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 1 |
Primary citation
Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications. Cookis, T., Lydecker, A., Sauer, P. et al. Nat Struct Mol Biol (2025) 32:393-404. DOI 10.1038/s41594-024-01452-x · 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
- 9C8U 3.1 Å, Human PRC2 - RvLEAM (short) (1:6 molar ratio), cross-linked 10 min
Browse structure collections
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