8VML: PRC2_AJ1-450
PRC2_AJ1-450 bound to H3K4me3. Determined by electron microscopy at 3.5 Å resolution. Released 15 Jan 2025.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 14,947
- Mol. weight
- 442 kDa
- Released
- 15 Jan 2025
Explore 8VML in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8VML contains 68 α-helices and 111 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 | 84-104 | 21 | |
| α-helix | 112-114 | 3 | |
| α-helix | 116-118 | 3 | |
| α-helix | 132-146 | 15 | |
| 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 | 230-233 | 4 | 1 |
| α-helix | 239-243 | 5 | |
| 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 | 427-433 | 7 | 4 |
| β-strand | 439-443 | 5 | 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 | 503-507 | 5 | |
| α-helix | 509 | 1 | |
| β-strand | 525-530 | 6 | 6 |
| α-helix | 536-538 | 3 | |
| α-helix | 540-542 | 3 | |
| β-strand | 558-560 | 3 | 6 |
| β-strand | 566 | 1 | 7 |
| β-strand | 573 | 1 | 7 |
| α-helix | 590-600 | 11 | |
| α-helix | 608-624 | 17 | |
| α-helix | 629-631 | 3 | |
| α-helix | 632-650 | 19 | |
| α-helix | 653-665 | 13 | |
| α-helix | 671-681 | 11 | |
Chain B: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 113-115 | 3 | |
| α-helix | 145-150 | 6 | |
| α-helix | 162-165 | 4 | |
Chain C: 26 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-60 | 42 | |
| α-helix | 66-68 | 3 | |
| β-strand | 82-85 | 4 | 8 |
| β-strand | 86-87 | 2 | 9 |
| β-strand | 94-97 | 4 | 8 |
| β-strand | 114-115 | 2 | 10 |
| β-strand | 120-121 | 2 | 11 |
| α-helix | 139-142 | 4 | |
| α-helix | 144-153 | 10 | |
| α-helix | 169-177 | 9 | |
| α-helix | 222-230 | 9 | |
| α-helix | 237-249 | 13 | |
| α-helix | 274-284 | 11 | |
| β-strand | 285-286 | 2 | 12 |
| β-strand | 291-292 | 2 | 12 |
| α-helix | 329-338 | 10 | |
| α-helix | 434-447 | 14 | |
| α-helix | 451-457 | 7 | |
| α-helix | 463-472 | 10 | |
| α-helix | 474-476 | 3 | |
| α-helix | 478-480 | 3 | |
| α-helix | 492-494 | 3 | |
| α-helix | 497-509 | 13 | |
| α-helix | 535-539 | 5 | |
| β-strand | 543 | 1 | 13 |
| β-strand | 556 | 1 | 13 |
| α-helix | 572-575 | 4 | |
| β-strand | 578 | 1 | 14 |
| α-helix | 605-608 | 4 | |
| α-helix | 611-613 | 3 | |
| β-strand | 614-618 | 5 | 7 |
| β-strand | 624-628 | 5 | 7 |
| β-strand | 632 | 1 | 15 |
| β-strand | 637-640 | 4 | 14 |
| β-strand | 644-647 | 4 | 11 |
| α-helix | 648-660 | 13 | |
| β-strand | 666-668 | 3 | 11 |
| β-strand | 673-676 | 4 | 11 |
| β-strand | 680-681 | 2 | 10 |
| α-helix | 683-686 | 4 | |
| α-helix | 687 | 1 | |
| β-strand | 688-689 | 2 | 16 |
| β-strand | 695-702 | 8 | 14 |
| β-strand | 705-712 | 8 | 14 |
| β-strand | 716 | 1 | 15 |
| α-helix | 720 | 1 | |
| β-strand | 721 | 1 | 7 |
| α-helix | 722 | 1 | |
| β-strand | 723-724 | 2 | 16 |
| α-helix | 730-736 | 7 | |
Chain I: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27 | 1 | 11 |
Chain L: 5 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 82-89 | 8 | 9 |
| β-strand | 100-101 | 2 | 17 |
| α-helix | 109-110 | 2 | |
| β-strand | 111-116 | 6 | 17 |
| β-strand | 120-126 | 7 | 17 |
| α-helix | 128-130 | 3 | |
| β-strand | 132-139 | 8 | 17 |
| β-strand | 147-154 | 8 | 18 |
| β-strand | 161-167 | 7 | 18 |
| β-strand | 172-176 | 5 | 18 |
| β-strand | 181-186 | 6 | 18 |
| β-strand | 193-198 | 6 | 19 |
| β-strand | 205-210 | 6 | 19 |
| β-strand | 215-219 | 5 | 19 |
| β-strand | 224-229 | 6 | 19 |
| β-strand | 239-244 | 6 | 20 |
| β-strand | 250-255 | 6 | 20 |
| β-strand | 260-264 | 5 | 20 |
| α-helix | 268-277 | 10 | |
| α-helix | 288-289 | 2 | |
| β-strand | 292-294 | 3 | 19 |
| β-strand | 299-301 | 3 | 20 |
| β-strand | 312-315 | 4 | 21 |
| β-strand | 318-323 | 6 | 21 |
| β-strand | 327-333 | 7 | 21 |
| α-helix | 340-342 | 3 | |
| β-strand | 350-357 | 8 | 21 |
| β-strand | 368-370 | 3 | 22 |
| β-strand | 376-379 | 4 | 22 |
| β-strand | 387-390 | 4 | 22 |
| β-strand | 402 | 1 | 22 |
| β-strand | 413-418 | 6 | 9 |
| β-strand | 424-429 | 6 | 9 |
| β-strand | 433-439 | 7 | 9 |
Chain N: 7 helices, 30 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-27 | 23 | |
| α-helix | 28-30 | 3 | |
| β-strand | 32-39 | 8 | 6 |
| β-strand | 48-49 | 2 | 23 |
| β-strand | 54 | 1 | 23 |
| β-strand | 61-68 | 8 | 23 |
| β-strand | 77-87 | 11 | 23 |
| β-strand | 115-123 | 9 | 23 |
| β-strand | 129-133 | 5 | 24 |
| β-strand | 136-143 | 8 | 24 |
| β-strand | 149-153 | 5 | 24 |
| α-helix | 154-156 | 3 | |
| α-helix | 161-162 | 2 | |
| β-strand | 174 | 1 | 25 |
| β-strand | 180-185 | 6 | 26 |
| β-strand | 192-197 | 6 | 26 |
| β-strand | 202-206 | 5 | 26 |
| β-strand | 218 | 1 | 25 |
| β-strand | 221-223 | 3 | 26 |
| β-strand | 230-235 | 6 | 27 |
| β-strand | 242-247 | 6 | 27 |
| β-strand | 251-256 | 6 | 27 |
| β-strand | 267-270 | 4 | 27 |
| β-strand | 276-281 | 6 | 28 |
| β-strand | 288-293 | 6 | 28 |
| β-strand | 298-302 | 5 | 28 |
| β-strand | 313 | 1 | 28 |
| β-strand | 320-325 | 6 | 29 |
| α-helix | 326 | 1 | |
| β-strand | 332-337 | 6 | 29 |
| β-strand | 342-346 | 5 | 29 |
| α-helix | 356-361 | 6 | |
| β-strand | 366-370 | 5 | 29 |
| β-strand | 379-381 | 3 | 6 |
| β-strand | 389-393 | 5 | 6 |
| β-strand | 398-404 | 7 | 6 |
| α-helix | 406-408 | 3 | |
Chain P: 10 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 174 | 1 | |
| α-helix | 176 | 1 | |
| α-helix | 183-185 | 3 | |
| α-helix | 192-209 | 18 | |
| α-helix | 211-215 | 5 | |
| β-strand | 219-223 | 5 | 30 |
| β-strand | 224-231 | 8 | 1 |
| β-strand | 237-243 | 7 | 1 |
| α-helix | 249-251 | 3 | |
| β-strand | 252-255 | 4 | 1 |
| α-helix | 256-258 | 3 | |
| β-strand | 264-268 | 5 | 30 |
| α-helix | 269-271 | 3 | |
| α-helix | 277-280 | 4 | |
| α-helix | 282-284 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| SUZ12 | A | protein | 739 | Homo sapiens | Q15022 (AlphaFold model) |
| JARID2 | B | protein | 1246 | Homo sapiens | Q92833 (AlphaFold model) |
| EZH2 | C | protein | 746 | Homo sapiens | Q15910 (AlphaFold model) |
| Histone H3 | I | protein | 22 | Homo sapiens | P68431 (AlphaFold model) |
| EED | L | protein | 441 | Homo sapiens | O75530 |
| RBAP48 | N | protein | 425 | Homo sapiens | Q09028 |
| AEPB2 | P | protein | 301 | Homo sapiens | Q6ZN18 |
Sequence of entity 1 (A), FASTA
>8VML_1 SUZ12 (chains A)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL
Sequence of entity 2 (B), FASTA
>8VML_2 JARID2 (chains B)
MSKERPKRNIIQKKYDDSDGIPWSEERVVRKVLYLSLKEFKNSQKRQHAEGIAGSLKTVN
GLLGNDQSKGLGPASEQSENEKDDASQVSSTSNDVSSSDFEEGPSRKRPRLQAQRKFAQS
QPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYFGSSQ
DEEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKEPVQK
HKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAATHHHPPLHRSAQDLR
KQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKRELVKDT
KPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPKSCTK
EVGGRQLREGLQLREGLRNSKRRLEEAHQAEKPQSPPKKMKGAAGPAEGPGKKAPAERGL
LNGHVKKEVPERSLERNRPKRATAGKSTPGRQAHGKADSASCENRSTSQPESVHKPQDSG
KAEKGGGKAGWAAMDEIPVLRPSAKEFHDPLIYIESVRAQVEKFGMCRVIPPPDWRPECK
LNDEMRFVTQIQHIHKLGRRWGPNVQRLACIKKHLKSQGITMDELPLIGGCELDLACFFR
LINEMGGMQQVTDLKKWNKLADMLRIPRTAQDRLAKLQEAYCQYLLSYDSLSPEEHRRLE
KEVLMEKEILEKRKGPLEGHTENDHHKFHPLPRFEPKNGLIHGVAPRNGFRSKLKEVGQA
QLKTGRRRLFAQEKEVVKEEEEDKGVLNDFHKCIYKGRSVSLTTFYRTARNIMSMCFSKE
PAPAEIEQEYWRLVEEKDCHVAVHCGKVDTNTHGSGFPVGKSEPFSRHGWNLTVLPNNTG
SILRHLGAVPGVTIPWLNIGMVFSTSCWSRDQNHLPYIDYLHTGADCIWYCIPAEEENKL
EDVVHTLLQANGTPGLQMLESNVMISPEVLCKEGIKVHRTVQQSGQFVVCFPGSFVSKVC
CGYSVSETVHFATTQWTSMGFETAKEMKRRHIAKPFSMEKLLYQIAQAEAKKENGPTLST
ISALLDELRDTELRQRRQLFEAGLHSSARYGSHDGSSTVADGKKKPRKWLQLETSERRCQ
ICQHLCYLSMVVQENENVVFCLECALRHVEKQKSCRGLKLMYRYDEEQIISLVNQICGKV
SGKNGSIENCLSKPTPKRGPRKRATVDVPPSRLSASSSSKSASSSS
Sequence of entity 3 (C), FASTA
>8VML_3 EZH2 (chains C)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH
ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPN
NSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKM
KPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA
PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQ
NFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS
CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK
YMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE
ELFFDYRYSQADALKYVGIEREMEIP
Sequence of entity 4 (I), FASTA
>8VML_4 Histone H3 (chains I)
QLATKAARKSAPATGGVKKPHR
Sequence of entity 5 (L), FASTA
>8VML_5 EED (chains L)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR
Sequence of entity 6 (N), FASTA
>8VML_6 RBAP48 (chains N)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS
Sequence of entity 7 (P), FASTA
>8VML_7 AEPB2 (chains P)
MYTRRYSSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSP
DLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCN
ASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHD
FFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDI
LPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKRTLIRKVFNLYLSK
Q
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
- 8VNV 3.1 Å, PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged
Browse structure collections
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