8TB9: PRC2-J119-450 monomer
PRC2-J119-450 monomer bound to H1-nucleosome. Determined by electron microscopy at 4.0 Å resolution. Released 25 Sept 2024.
- Method
- Electron microscopy
- Resolution
- 4.0 Å
- Organisms
- Homo sapiens, synthetic construct, Xenopus laevis
- Chains
- 17
- Atoms
- 30,224
- Mol. weight
- 591.04 kDa
- Ligands
- SAH
- Released
- 25 Sept 2024
Explore 8TB9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8TB9 contains 105 α-helices and 143 β-strands across 15 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: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-37 | 11 | |
| β-strand | 44-45 | 2 | 1 |
| α-helix | 46-56 | 11 | |
| α-helix | 63-77 | 15 | |
| β-strand | 81-84 | 4 | 1 |
| β-strand | 91-93 | 3 | 1 |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 146-150 | 5 | |
Chain D: 15 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 83-106 | 24 | |
| α-helix | 112-114 | 3 | |
| α-helix | 134-145 | 12 | |
| β-strand | 158-165 | 8 | 2 |
| β-strand | 184-192 | 9 | 3 |
| β-strand | 203-211 | 9 | 3 |
| β-strand | 230-232 | 3 | 2 |
| α-helix | 239-244 | 6 | |
| β-strand | 245-253 | 9 | 3 |
| β-strand | 296 | 1 | 4 |
| β-strand | 297-300 | 4 | 3 |
| β-strand | 302 | 1 | 5 |
| β-strand | 308 | 1 | 5 |
| β-strand | 314-318 | 5 | 2 |
| β-strand | 320 | 1 | 4 |
| β-strand | 354-360 | 7 | 2 |
| β-strand | 428-434 | 7 | 6 |
| β-strand | 438-443 | 6 | 6 |
| β-strand | 449 | 1 | 7 |
| β-strand | 456 | 1 | 7 |
| α-helix | 460-470 | 11 | |
| β-strand | 474-478 | 5 | 6 |
| β-strand | 485-491 | 7 | 6 |
| α-helix | 503-505 | 3 | |
| α-helix | 509 | 1 | |
| β-strand | 525-530 | 6 | 8 |
| α-helix | 536-538 | 3 | |
| α-helix | 540-547 | 8 | |
| β-strand | 557-559 | 3 | 8 |
| β-strand | 566-567 | 2 | 9 |
| β-strand | 572-573 | 2 | 9 |
| α-helix | 576-578 | 3 | |
| α-helix | 590-602 | 13 | |
| α-helix | 608-624 | 17 | |
| α-helix | 629-650 | 22 | |
| α-helix | 653-665 | 13 | |
| α-helix | 671-681 | 11 | |
Chain E: 29 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-62 | 45 | |
| α-helix | 66-68 | 3 | |
| α-helix | 75-77 | 3 | |
| β-strand | 82-85 | 4 | 10 |
| β-strand | 86-87 | 2 | 11 |
| α-helix | 92-93 | 2 | |
| β-strand | 94-97 | 4 | 10 |
| β-strand | 100 | 1 | 12 |
| α-helix | 101-103 | 3 | |
| β-strand | 114-115 | 2 | 13 |
| β-strand | 119-121 | 3 | 14 |
| α-helix | 166-167 | 2 | |
| α-helix | 168-179 | 12 | |
| α-helix | 221-230 | 10 | |
| α-helix | 237-247 | 11 | |
| α-helix | 274-284 | 11 | |
| β-strand | 285-286 | 2 | 15 |
| β-strand | 291-292 | 2 | 15 |
| α-helix | 334-342 | 9 | |
| α-helix | 439-452 | 14 | |
| α-helix | 456-462 | 7 | |
| α-helix | 472-481 | 10 | |
| α-helix | 483-485 | 3 | |
| α-helix | 501-511 | 11 | |
| α-helix | 512-516 | 5 | |
| α-helix | 540-543 | 4 | |
| α-helix | 547 | 1 | |
| β-strand | 548 | 1 | 16 |
| α-helix | 549 | 1 | |
| β-strand | 561 | 1 | 16 |
| α-helix | 577-580 | 4 | |
| β-strand | 583 | 1 | 17 |
| α-helix | 584-586 | 3 | |
| α-helix | 610-613 | 4 | |
| α-helix | 616-618 | 3 | |
| β-strand | 619-623 | 5 | 9 |
| β-strand | 629-633 | 5 | 9 |
| β-strand | 637 | 1 | 18 |
| β-strand | 642 | 1 | 17 |
| β-strand | 648-652 | 5 | 14 |
| α-helix | 653-664 | 12 | |
| β-strand | 671-672 | 2 | 14 |
| β-strand | 678-681 | 4 | 14 |
| β-strand | 685-686 | 2 | 13 |
| α-helix | 688-691 | 4 | |
| β-strand | 693-694 | 2 | 19 |
| β-strand | 700-707 | 8 | 17 |
| β-strand | 710-717 | 8 | 17 |
| β-strand | 721 | 1 | 18 |
| α-helix | 725 | 1 | |
| β-strand | 726 | 1 | 9 |
| α-helix | 727 | 1 | |
| β-strand | 728-729 | 2 | 19 |
| α-helix | 735-741 | 7 | |
Chain G: 6 helices, 36 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 82-86 | 5 | 20 |
| β-strand | 88-89 | 2 | 11 |
| α-helix | 94 | 1 | |
| β-strand | 95 | 1 | 21 |
| α-helix | 96 | 1 | |
| β-strand | 99-101 | 3 | 12 |
| β-strand | 112-116 | 5 | 12 |
| β-strand | 120-126 | 7 | 12 |
| α-helix | 128-130 | 3 | |
| β-strand | 132-139 | 8 | 12 |
| β-strand | 147-154 | 8 | 22 |
| β-strand | 161-167 | 7 | 22 |
| β-strand | 172-176 | 5 | 22 |
| β-strand | 181-186 | 6 | 22 |
| β-strand | 193-198 | 6 | 23 |
| β-strand | 205-210 | 6 | 23 |
| β-strand | 215-219 | 5 | 23 |
| β-strand | 224-229 | 6 | 23 |
| α-helix | 231-233 | 3 | |
| β-strand | 239-244 | 6 | 24 |
| β-strand | 250-255 | 6 | 24 |
| β-strand | 260-264 | 5 | 24 |
| α-helix | 268-277 | 10 | |
| α-helix | 288-289 | 2 | |
| β-strand | 293-294 | 2 | 23 |
| β-strand | 299 | 1 | 24 |
| β-strand | 309-311 | 3 | 25 |
| β-strand | 314-315 | 2 | 25 |
| β-strand | 318-323 | 6 | 25 |
| β-strand | 328-333 | 6 | 25 |
| β-strand | 350-352 | 3 | 25 |
| β-strand | 369-370 | 2 | 26 |
| β-strand | 376-379 | 4 | 26 |
| β-strand | 385 | 1 | 27 |
| β-strand | 387-390 | 4 | 26 |
| β-strand | 402 | 1 | 26 |
| β-strand | 405 | 1 | 27 |
| β-strand | 413-418 | 6 | 20 |
| β-strand | 424-429 | 6 | 20 |
| β-strand | 431 | 1 | 21 |
| β-strand | 433 | 1 | 11 |
| β-strand | 434-439 | 6 | 20 |
Chain I: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27 | 1 | 14 |
| α-helix | 36-39 | 4 | |
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 28 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 29 |
| α-helix | 121-130 | 10 | |
Chain J: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 29 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 28 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 30 |
Chain O: 6 helices, 31 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-27 | 23 | |
| β-strand | 32-39 | 8 | 8 |
| β-strand | 47-49 | 3 | 31 |
| β-strand | 54 | 1 | 31 |
| β-strand | 61-68 | 8 | 31 |
| β-strand | 77-87 | 11 | 31 |
| β-strand | 115-123 | 9 | 31 |
| β-strand | 129-133 | 5 | 32 |
| β-strand | 136-143 | 8 | 32 |
| β-strand | 149 | 1 | 33 |
| β-strand | 150-153 | 4 | 32 |
| β-strand | 172-173 | 2 | 33 |
| β-strand | 183-185 | 3 | 34 |
| β-strand | 192-196 | 5 | 34 |
| β-strand | 202-206 | 5 | 34 |
| α-helix | 207-209 | 3 | |
| β-strand | 216-217 | 2 | 33 |
| β-strand | 221-223 | 3 | 34 |
| β-strand | 230-235 | 6 | 35 |
| β-strand | 242-247 | 6 | 35 |
| β-strand | 251-256 | 6 | 35 |
| β-strand | 267-270 | 4 | 35 |
| β-strand | 279-281 | 3 | 36 |
| β-strand | 289-292 | 4 | 36 |
| β-strand | 298-301 | 4 | 36 |
| β-strand | 311-313 | 3 | 36 |
| β-strand | 320-325 | 6 | 37 |
| α-helix | 326 | 1 | |
| β-strand | 332-337 | 6 | 37 |
| β-strand | 342-346 | 5 | 37 |
| α-helix | 347-349 | 3 | |
| α-helix | 356-359 | 4 | |
| β-strand | 366-370 | 5 | 37 |
| α-helix | 376 | 1 | |
| β-strand | 377-383 | 7 | 8 |
| β-strand | 386-394 | 9 | 8 |
| β-strand | 398-404 | 7 | 8 |
7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H1.0 | A | protein | 197 | Homo sapiens | P07305 (AlphaFold model) |
| Protein Jumonji | B | protein | 334 | Homo sapiens | Q92833 (AlphaFold model) |
| Polycomb protein SUZ12 | D | protein | 619 | Homo sapiens | Q15022 (AlphaFold model) |
| Histone-lysine N-methyltransferase EZH2 | E | protein | 753 | Homo sapiens | Q15910 (AlphaFold model) |
| Polycomb protein EED | G | protein | 441 | Homo sapiens | O75530 |
| DNA (226-mer) | H | DNA | 215 | synthetic construct | |
| Histone H3.2 | I, W | protein | 136 | Xenopus laevis | P84233 |
| Histone H4 | J, X | protein | 106 | Xenopus laevis | P62799 |
| Histone-binding protein RBBP4 | O | protein | 425 | Homo sapiens | Q09028 |
| Histone H2A type 1 | R, U | protein | 133 | Xenopus laevis | P06897 |
| Histone H2B 1.1 | S, V | protein | 123 | Xenopus laevis | P02281 |
| DNA (226-mer) | T | DNA | 215 | synthetic construct | |
1 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8TB9_1 Histone H1.0 (chains A)
GSHMTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSH
YKVGENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKV
ATPKKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAK
PVKPKAKSSAKRAGKKK
Sequence of entity 2 (B), FASTA
>8TB9_2 Protein Jumonji (chains B)
MVQSQPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYF
GSSQDEEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKE
PVQKHKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAATHHHPPLHRSA
QDLRKQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKREL
VKDTKPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPK
SCTKEVGGRQLREGLQLREGLRNSKRRLEEAHQA
Sequence of entity 3 (D), FASTA
>8TB9_3 Polycomb protein SUZ12 (chains D)
MVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTN
IKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEV
LLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVK
SYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNR
RLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETN
DKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKL
RIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGAR
IDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLES
EDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDV
NEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDF
NLISIMSIDKAVTKLREMQ
Sequence of entity 4 (E), FASTA
>8TB9_4 Histone-lysine N-methyltransferase EZH2 (chains E)
SNAGQTGKKSEKGPVACRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQ
EWKQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQ
NFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNAL
GQYNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAE
ELKEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHR
KCNYSFHATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGR
RRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSR
CQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKE
SSIIAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSS
CPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADH
WDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADR
RGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAK
RAIQTGEELFFDYRYSQADALKYVGIEREMEIP
Sequence of entity 5 (G), FASTA
>8TB9_5 Polycomb protein EED (chains G)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR
Sequence of entity 6 (H), FASTA
>8TB9_6 DNA (226-MER) (chains H)
ATCGGGAGCTCCGACCGAATGACATGCATGCATACAGGATGTATATACCTGACACGTGCC
TGGAGACTAGGGAGTAACCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGT
TTAAGCGGTGCTAGAGCTGCCTACGACCAATGGAGCGGCCTCGGCACCGGGATCCCCCAG
CCGCCGGCAGCGCAGCGCCTGACGGGCACACAGTC
Sequence of entity 7 (I, W), FASTA
>8TB9_7 Histone H3.2 (chains I, W)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 8 (J, X), FASTA
>8TB9_8 Histone H4 (chains J, X)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGGSSG
Sequence of entity 9 (O), FASTA
>8TB9_9 Histone-binding protein RBBP4 (chains O)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS
Sequence of entity 10 (R, U), FASTA
>8TB9_10 Histone H2A type 1 (chains R, U)
SNAMSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLL
PKCTESSKSAKSK
Sequence of entity 11 (S, V), FASTA
>8TB9_11 Histone H2B 1.1 (chains S, V)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK
Sequence of entity 12 (T), FASTA
>8TB9_12 DNA (226-MER) (chains T)
GACTGTGTGCCCGTCAGACGCTGCGCCGCCGGCGGCCGGAGAATCCCGGTGCCGAGGCCG
CCCTATTGGTCGTAGACAGCCCCAGCACCGCCTAAACGCACGTACGCGCCGTCCCCCGCG
TTTTAACCGCCAAGGGGATTACCCCCCAGTCCCCAGGCACGTGCCAGATATATACATCCC
GTACGCACGCACATCATTCGATCGGAGCTCCCGAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 1 |
Primary citation
Activation of automethylated PRC2 by dimerization on chromatin. Sauer, P.V., Pavlenko, E., Cookis, T. et al. Mol Cell (2024) 84:3885-3898.e8. DOI 10.1016/j.molcel.2024.08.025 · PubMed
Other PDB entries of the same protein (UniProt P07305 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7COW 2.86 Å, 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0
- 7K5X 2.93 Å, Cryo-EM structure of a chromatosome containing human linker histone H1.0
- 6LAB 3.2 Å, 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0
- 7XX6 3.39 Å, Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment)
- 6LA8 3.4 Å, 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0
- 7XVL 3.51 Å, Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment)
- 30FM 3.6 Å, Structure of histone H1 in an import-chaperone complex with importin beta and importin 7…
- 30HD 3.6 Å, Structure of histone H1 in an import-chaperone complex with importin beta and importin 7…
- 6LA9 3.7 Å, 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0…
- 6LA2 3.89 Å, 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0
- 9IPU 4.3 Å, cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to…
- 7DBP 4.5 Å, Linker histone defines structure and self-association behaviour of the 177 bp human…
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