7KSO: PRC2:EZH1-AEBP2-JARID2
Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2. Determined by electron microscopy at 3.9 Å resolution. Released 3 Feb 2021.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 13,075
- Mol. weight
- 439.07 kDa
- Ligands
- ZN
- Released
- 3 Feb 2021
Explore 7KSO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7KSO contains 42 α-helices and 108 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: 15 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-61 | 27 | |
| α-helix | 66-68 | 3 | |
| β-strand | 82-85 | 4 | 1 |
| α-helix | 93-94 | 2 | |
| β-strand | 95-98 | 4 | 1 |
| β-strand | 100-101 | 2 | 2 |
| β-strand | 115-116 | 2 | 3 |
| β-strand | 121-122 | 2 | 4 |
| α-helix | 287-290 | 4 | |
| α-helix | 292-297 | 6 | |
| β-strand | 298 | 1 | 5 |
| β-strand | 305 | 1 | 5 |
| α-helix | 316-318 | 3 | |
| α-helix | 436-449 | 14 | |
| α-helix | 453-460 | 8 | |
| α-helix | 465-473 | 9 | |
| α-helix | 536-539 | 4 | |
| β-strand | 544 | 1 | 6 |
| β-strand | 557 | 1 | 6 |
| α-helix | 559-561 | 3 | |
| α-helix | 573-576 | 4 | |
| α-helix | 606-609 | 4 | |
| β-strand | 615-619 | 5 | 7 |
| β-strand | 625-629 | 5 | 7 |
| β-strand | 638-640 | 3 | 8 |
| β-strand | 645-647 | 3 | 4 |
| α-helix | 649-662 | 14 | |
| β-strand | 668 | 1 | 4 |
| β-strand | 675-677 | 3 | 4 |
| β-strand | 681-682 | 2 | 3 |
| α-helix | 684-687 | 4 | |
| β-strand | 689 | 1 | 9 |
| β-strand | 696-703 | 8 | 8 |
| β-strand | 706-713 | 8 | 8 |
| β-strand | 722 | 1 | 7 |
| β-strand | 724 | 1 | 9 |
Chain B: 4 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 83-89 | 7 | 10 |
| β-strand | 98-101 | 4 | 2 |
| α-helix | 110-111 | 2 | |
| β-strand | 112-116 | 5 | 2 |
| β-strand | 121-125 | 5 | 2 |
| β-strand | 134-139 | 6 | 2 |
| β-strand | 149-154 | 6 | 11 |
| β-strand | 161-166 | 6 | 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 | 251-255 | 5 | 13 |
| β-strand | 260-262 | 3 | 13 |
| α-helix | 268-278 | 11 | |
| β-strand | 292-293 | 2 | 12 |
| β-strand | 299 | 1 | 13 |
| β-strand | 312-315 | 4 | 14 |
| β-strand | 318-321 | 4 | 14 |
| β-strand | 327-333 | 7 | 14 |
| α-helix | 340-342 | 3 | |
| β-strand | 350-357 | 8 | 14 |
| β-strand | 368-369 | 2 | 15 |
| β-strand | 376-379 | 4 | 15 |
| β-strand | 386-390 | 5 | 15 |
| α-helix | 396-398 | 3 | |
| β-strand | 402-404 | 3 | 15 |
| β-strand | 413-418 | 6 | 10 |
| β-strand | 424-429 | 6 | 10 |
| β-strand | 433-438 | 6 | 10 |
Chain C: 15 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 80-106 | 27 | |
| α-helix | 112-114 | 3 | |
| α-helix | 127-130 | 4 | |
| α-helix | 137-144 | 8 | |
| β-strand | 156-165 | 10 | 16 |
| β-strand | 184-192 | 9 | 17 |
| α-helix | 193-195 | 3 | |
| α-helix | 201-202 | 2 | |
| β-strand | 203-211 | 9 | 17 |
| β-strand | 230-234 | 5 | 16 |
| β-strand | 245-254 | 10 | 17 |
| β-strand | 296 | 1 | 18 |
| β-strand | 297 | 1 | 17 |
| β-strand | 300 | 1 | 17 |
| β-strand | 302 | 1 | 19 |
| β-strand | 308 | 1 | 19 |
| β-strand | 313-318 | 6 | 16 |
| β-strand | 320 | 1 | 18 |
| β-strand | 354-359 | 6 | 16 |
| β-strand | 429-431 | 3 | 20 |
| β-strand | 441 | 1 | 20 |
| β-strand | 443 | 1 | 21 |
| α-helix | 460-469 | 10 | |
| β-strand | 474-479 | 6 | 20 |
| β-strand | 486-491 | 6 | 20 |
| α-helix | 503-505 | 3 | |
| β-strand | 525-528 | 4 | 22 |
| β-strand | 557-560 | 4 | 22 |
| β-strand | 566 | 1 | 7 |
| α-helix | 572 | 1 | |
| β-strand | 573 | 1 | 7 |
| α-helix | 574-575 | 2 | |
| α-helix | 590-601 | 12 | |
| α-helix | 608-623 | 16 | |
| α-helix | 631-648 | 18 | |
| α-helix | 653-665 | 13 | |
| α-helix | 671-685 | 15 | |
Chain D: 4 helices, 30 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-27 | 22 | |
| α-helix | 28-30 | 3 | |
| β-strand | 32-39 | 8 | 22 |
| β-strand | 47-49 | 3 | 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 | 130-132 | 3 | 24 |
| β-strand | 139-142 | 4 | 24 |
| β-strand | 149-153 | 5 | 24 |
| β-strand | 171-173 | 3 | 24 |
| β-strand | 183-185 | 3 | 25 |
| β-strand | 192-197 | 6 | 25 |
| β-strand | 201-206 | 6 | 25 |
| β-strand | 221-223 | 3 | 25 |
| β-strand | 230-235 | 6 | 26 |
| β-strand | 242-247 | 6 | 26 |
| β-strand | 251-256 | 6 | 26 |
| β-strand | 267-269 | 3 | 26 |
| β-strand | 276-281 | 6 | 27 |
| β-strand | 288-293 | 6 | 27 |
| β-strand | 297-302 | 6 | 27 |
| β-strand | 311-313 | 3 | 27 |
| β-strand | 320-322 | 3 | 28 |
| β-strand | 332-335 | 4 | 29 |
| β-strand | 336-337 | 2 | 28 |
| β-strand | 342-346 | 5 | 29 |
| α-helix | 356-361 | 6 | |
| β-strand | 366-370 | 5 | 29 |
| β-strand | 377-382 | 6 | 22 |
| β-strand | 389-394 | 6 | 22 |
| β-strand | 398-404 | 7 | 22 |
| α-helix | 406-409 | 4 | |
Chain E: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 400-417 | 18 | |
| α-helix | 419-423 | 5 | |
| β-strand | 428-431 | 4 | 30 |
| β-strand | 434-438 | 5 | 16 |
| β-strand | 446-449 | 4 | 16 |
| β-strand | 460-462 | 3 | 16 |
| α-helix | 469-471 | 3 | |
| β-strand | 472-475 | 4 | 30 |
Chain F: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 153 | 1 | 21 |
| α-helix | 154-163 | 10 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone-lysine N-methyltransferase EZH1 | A | protein | 747 | Homo sapiens | Q92800 (AlphaFold model) |
| Polycomb protein EED | B | protein | 441 | Homo sapiens | O75530 (AlphaFold model) |
| Polycomb protein SUZ12 | C | protein | 739 | Homo sapiens | Q15022 (AlphaFold model) |
| Histone-binding protein RBBP4 | D | protein | 425 | Homo sapiens | Q09028 (AlphaFold model) |
| Zinc finger protein AEBP2 | E | protein | 295 | Homo sapiens | Q6ZN18 |
| Protein Jumonji | F | protein | 1246 | Homo sapiens | Q92833 |
Sequence of entity 1 (A), FASTA
>7KSO_1 Histone-lysine N-methyltransferase EZH1 (chains A)
MEIPNPPTSKCITYWKRKVKSEYMRLRQLKRLQANMGAKALYVANFAKVQEKTQILNEEW
KKLRVQPVQSMKPVSGHPFLKKCTIESIFPGFASQHMLMRSLNTVALVPIMYSWSPLQQN
FMVEDETVLCNIPYMGDEVKEEDETFIEELINNYDGKVHGEEEMIPGSVLISDAVFLELV
DALNQYSDEEEEGHNDTSDGKQDDSKEDLPVTRKRKRHAIEGNKKSSKKQFPNDMIFSAI
ASMFPENGVPDDMKERYRELTEMSDPNALPPQCTPNIDGPNAKSVQREQSLHSFHTLFCR
RCFKYDCFLHPFHATPNVYKRKNKEIKIEPEPCGTDCFLLLEGAKEYAMLHNPRSKCSGR
RRRRHHIVSASCSNASASAVAETKEGDSDRDTGNDWASSSSEANSRCQTPTKQKASPAPP
QLCVVEAPSEPVEWTGAEESLFRVFHGTYFNNFCSIARLLGTKTCKQVFQFAVKESLILK
LPTDELMNPSQKKKRKHRLWAAHCRKIQLKKDNSSTQVYNYQPCDHPDRPCDSTCPCIMT
QNFCEKFCQCNPDCQNRFPGCRCKTQCNTKQCPCYLAVRECDPDLCLTCGASEHWDCKVV
SCKNCSIQRGLKKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYD
KYMSSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVVMVNGDHRIGIFAKRAIQAG
EELFFDYRYSQADALKYVGIERETDVL
Sequence of entity 2 (B), FASTA
>7KSO_2 Polycomb protein EED (chains B)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR
Sequence of entity 3 (C), FASTA
>7KSO_3 Polycomb protein SUZ12 (chains C)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL
Sequence of entity 4 (D), FASTA
>7KSO_4 Histone-binding protein RBBP4 (chains D)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS
Sequence of entity 5 (E), FASTA
>7KSO_5 Zinc finger protein AEBP2 (chains E)
MSSDGEPLSRMDSEDSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQC
QACFNSSPDLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPF
KCVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRR
RSLPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLL
LHWMPEDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR
Sequence of entity 6 (F), FASTA
>7KSO_6 Protein Jumonji (chains F)
MSKERPKRNIIQKKYDDSDGIPWSEERVVRKVLYLSLKEFKNSQKRQHAEGIAGSLKTVN
GLLGNDQSKGLGPASEQSENEKDDASQVSSTSNDVSSSDFEEGPSRKRPRLQAQRKFAQS
QPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYFGSSQ
DEEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKEPVQK
HKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAATHHHPPLHRSAQDLR
KQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKRELVKDT
KPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPKSCTK
EVGGRQLREGLQLREGLRNSKRRLEEAHQAEKPQSPPKKMKGAAGPAEGPGKKAPAERGL
LNGHVKKEVPERSLERNRPKRATAGKSTPGRQAHGKADSASCENRSTSQPESVHKPQDSG
KAEKGGGKAGWAAMDEIPVLRPSAKEFHDPLIYIESVRAQVEKFGMCRVIPPPDWRPECK
LNDEMRFVTQIQHIHKLGRRWGPNVQRLACIKKHLKSQGITMDELPLIGGCELDLACFFR
LINEMGGMQQVTDLKKWNKLADMLRIPRTAQDRLAKLQEAYCQYLLSYDSLSPEEHRRLE
KEVLMEKEILEKRKGPLEGHTENDHHKFHPLPRFEPKNGLIHGVAPRNGFRSKLKEVGQA
QLKTGRRRLFAQEKEVVKEEEEDKGVLNDFHKCIYKGRSVSLTTFYRTARNIMSMCFSKE
PAPAEIEQEYWRLVEEKDCHVAVHCGKVDTNTHGSGFPVGKSEPFSRHGWNLTVLPNNTG
SILRHLGAVPGVTIPWLNIGMVFSTSCWSRDQNHLPYIDYLHTGADCIWYCIPAEEENKL
EDVVHTLLQANGTPGLQMLESNVMISPEVLCKEGIKVHRTVQQSGQFVVCFPGSFVSKVC
CGYSVSETVHFATTQWTSMGFETAKEMKRRHIAKPFSMEKLLYQIAQAEAKKENGPTLST
ISALLDELRDTELRQRRQLFEAGLHSSARYGSHDGSSTVADGKKKPRKWLQLETSERRCQ
ICQHLCYLSMVVQENENVVFCLECALRHVEKQKSCRGLKLMYRYDEEQIISLVNQICGKV
SGKNGSIENCLSKPTPKRGPRKRATVDVPPSRLSASSSSKSASSSS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
Primary citation
Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction. Grau, D., Zhang, Y., Lee, C.H. et al. Nat Commun (2021) 12:714-714. DOI 10.1038/s41467-020-20775-z · PubMed
Other PDB entries of the same protein (UniProt Q92800 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7TD5 2.99 Å, Structure of human PRC2-EZH1 containing phosphorylated SUZ12
- 7KSR 4.1 Å, PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome
- 7KTP 4.8 Å, PRC2:EZH1_B from a dimeric PRC2 bound to a nucleosome
Browse structure collections
About this viewer
MolViewer shows 7KSO directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.