28OE: Human PRC1.4
Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome. Determined by electron microscopy at 2.74 Å resolution. Released 16 Sept 2026.
- Method
- Electron microscopy
- Resolution
- 2.74 Å
- Organisms
- Homo sapiens, Xenopus
- Chains
- 15
- Atoms
- 17,632
- Mol. weight
- 408.77 kDa
- Ligands
- ZN
- Released
- 16 Sept 2026
Explore 28OE in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
28OE contains 74 α-helices and 61 β-strands across 13 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: 0 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-38 | 3 | 1 |
| β-strand | 41-43 | 3 | 1 |
| β-strand | 44-45 | 2 | 2 |
Chain B: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 128-134 | 7 | 1 |
| β-strand | 137-143 | 7 | 1 |
Chain C: 11 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-20 | 3 | |
| α-helix | 21-24 | 4 | |
| β-strand | 37-40 | 4 | 3 |
| α-helix | 42-45 | 4 | |
| β-strand | 50-51 | 2 | 4 |
| β-strand | 56-57 | 2 | 4 |
| β-strand | 61-64 | 4 | 5 |
| β-strand | 70-72 | 3 | 5 |
| α-helix | 73-81 | 9 | |
| β-strand | 86 | 1 | 6 |
| β-strand | 93 | 1 | 6 |
| α-helix | 97-99 | 3 | |
| β-strand | 100-102 | 3 | 5 |
| α-helix | 104-113 | 10 | |
| α-helix | 118-135 | 18 | |
| β-strand | 226-230 | 5 | 1 |
| α-helix | 234-237 | 4 | |
| β-strand | 246-250 | 5 | 1 |
| β-strand | 255 | 1 | 7 |
| α-helix | 256-275 | 20 | |
| α-helix | 288-290 | 3 | |
| β-strand | 295 | 1 | 8 |
| β-strand | 305 | 1 | 8 |
| β-strand | 310 | 1 | 7 |
| α-helix | 311-317 | 7 | |
Chain D: 13 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-8 | 4 | 3 |
| α-helix | 9-12 | 4 | |
| α-helix | 13-15 | 3 | |
| β-strand | 17 | 1 | 9 |
| β-strand | 24 | 1 | 9 |
| β-strand | 28-31 | 4 | 10 |
| β-strand | 37-39 | 3 | 10 |
| α-helix | 40-46 | 7 | |
| α-helix | 47-49 | 3 | |
| β-strand | 52 | 1 | 11 |
| β-strand | 59 | 1 | 11 |
| α-helix | 65-68 | 4 | |
| β-strand | 69-71 | 3 | 10 |
| α-helix | 74-82 | 9 | |
| α-helix | 86-90 | 5 | |
| α-helix | 93-100 | 8 | |
| α-helix | 124-127 | 4 | |
| β-strand | 130-138 | 9 | 2 |
| α-helix | 140-143 | 4 | |
| β-strand | 162-167 | 6 | 2 |
| β-strand | 171 | 1 | 12 |
| α-helix | 172-182 | 11 | |
| β-strand | 189-195 | 7 | 2 |
| β-strand | 198-199 | 2 | 2 |
| α-helix | 200-201 | 2 | |
| β-strand | 205 | 1 | 12 |
| α-helix | 206-213 | 8 | |
| β-strand | 221-229 | 9 | 2 |
Chain E: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-15 | 13 | |
| β-strand | 21-25 | 5 | 13 |
| β-strand | 32-38 | 7 | 13 |
| β-strand | 49-55 | 7 | 13 |
| α-helix | 60-62 | 3 | |
| β-strand | 66-69 | 4 | 13 |
| β-strand | 75 | 1 | 14 |
| β-strand | 78 | 1 | 14 |
| β-strand | 84 | 1 | 14 |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 132-140 | 9 | |
| α-helix | 141-146 | 6 | |
Chains F and J: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 15 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 16 |
| α-helix | 121-131 | 11 | |
Chain G: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 16 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 15 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 17 |
Chain H: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-14 | 2 | |
| α-helix | 17-21 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 18 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 19 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 20 |
| α-helix | 113-115 | 3 | |
| α-helix | 117-118 | 2 | |
4 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 |
|---|
| Isoform 2 of Polyhomeotic-like protein 2 | A | protein | 327 | Homo sapiens | Q8IXK0 (AlphaFold model) |
| Chromobox 7 | B | protein | 162 | Homo sapiens | B0QYP2 (AlphaFold model) |
| E3 ubiquitin-protein ligase RING2 | C | protein | 340 | Homo sapiens | Q99496 (AlphaFold model) |
| Polycomb complex protein BMI-1 | D | protein | 336 | Homo sapiens | P35226 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 D3 | E | protein | 147 | Homo sapiens | Q4R5N4 |
| Histone H3 | F, J | protein | 135 | Xenopus | A0A310TTQ1 |
| Histone H4 | G, K | protein | 102 | Xenopus | P62798 |
| Histone H2A | H, L | protein | 129 | Xenopus | Q6AZJ8 |
| Histone H2B | I, M | protein | 122 | Xenopus | A0A1B8Y854 |
| DNA (151-mer) | N | DNA | 248 | Homo sapiens | |
| DNA (151-mer) | O | DNA | 248 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>28OE_1 Isoform 2 of Polyhomeotic-like protein 2 (chains A)
GPDSMTSGNGNSASSIAGTAPQNGENKPPQAIVKPQILTHVIEGFVIQEGAEPFPVGRSS
LLVGNLKKKYAQGFLPEKLPQQDHTTTTDSEMEEPYLQESKEEGAPLKLKCELCGRVDFA
YKFKRSKRFCSMACAKRYNVGCTKRVGLFHSDRSKLQKAGAATHNRRRASKASLPPLTKD
TKKQPTGTVPLSVTAALQLTHSQEDSSRCSDNSSYEEPLSPISASSSTSRRRQGQRDLEL
PDMHMRDLVGMGHHFLPSEPTKWNVEDVYEFIRSLPGCQEIAEEFRAQEIDGQALLLLKE
DHLMSAMNIKEGPAEKIYARISMLKDS
Sequence of entity 2 (B), FASTA
>28OE_2 Chromobox 7 (chains B)
GPDSMELSAIGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMA
YEEKEERDRASGYRKRGPKPKRLLLQEPPAPDVLQAAGEWEPAAQPPEEEADADLAEGPP
PWTPALPSSEVTVTDITANSITVTFREAQAAEGFFRDRSGKF
Sequence of entity 3 (C), FASTA
>28OE_3 E3 ubiquitin-protein ligase RING2 (chains C)
GPDSMSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLD
MLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPS
RDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDS
SHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTL
MEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIA
TASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK
Sequence of entity 4 (D), FASTA
>28OE_4 Polycomb complex protein BMI-1 (chains D)
MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQV
HKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADE
DKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLR
SKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQR
DGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSP
SGNHQSSFANRPRKSSVNGSSATSSGGSGSLEVLFQ
Sequence of entity 5 (E), FASTA
>28OE_5 Ubiquitin-conjugating enzyme E2 D3 (chains E)
MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLV
PEIARIYKTDRDKYNRISREWTQKYAM
Sequence of entity 6 (F, J), FASTA
>28OE_6 Histone H3 (chains F, J)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 7 (G, K), FASTA
>28OE_7 Histone H4 (chains G, K)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 8 (H, L), FASTA
>28OE_8 Histone H2A (chains H, L)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 9 (I, M), FASTA
>28OE_9 Histone H2B (chains I, M)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 10 (N), FASTA
>28OE_10 DNA (151-MER) (chains N)
ATATCTCGGGCTTATGTGATGGACCCTATACGCGGCGGACCTGGAGAATCCCGGTGCCGA
GGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCC
CCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATAC
ATCCTGTGTATTTATTGAACAGCGACTCGGGATATCTCTAGAGTCGACCTGCAGGCATGC
AAGCTTGG
Sequence of entity 11 (O), FASTA
>28OE_11 DNA (151-MER) (chains O)
CCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGATATCCCGAGTCGCTGTTCAATAAATA
CACAGGATGTATATATCTGACACGTGCCTGGAGATTAGGGAGTAATCCCCTTGGCGGTTA
AAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATT
GAGCGGCCTCGGCACCGGGATTCTCCAGGTCCGCCGCGTATAGGGTCCATCACATAAGCC
CGAGATAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Cryo-EM structure, enzymatic activity and genome targeting of canonical PRC1. Ciapponi, M., Cafiso, M., Schkolziger, S. et al. Nat Struct Mol Biol (2026). DOI 10.1038/s41594-026-01885-6 · PubMed
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