9V9Q: CPRC1-UbcH5c E3-E2 complex
Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome. Determined by electron microscopy at 2.8 Å resolution. Released 10 Jun 2026.
- Method
- Electron microscopy
- Resolution
- 2.8 Å
- Organisms
- Xenopus laevis, Homo sapiens
- Chains
- 15
- Atoms
- 15,996
- Mol. weight
- 307.85 kDa
- Ligands
- ZN
- Released
- 10 Jun 2026
Explore 9V9Q in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9V9Q contains 59 α-helices and 54 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: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 46-56 | 11 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 113-115 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
| α-helix | 117-118 | 2 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 10 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 9 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
5 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 H3 | A, E | protein | 136 | Xenopus laevis | A0A310TTQ1 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 130 | Xenopus laevis | Q6AZJ8 (AlphaFold model) |
| Histone H2B | D, H | protein | 126 | Xenopus laevis | A0A8J0TWI5 (AlphaFold model) |
| DNA (144-mer) | I | DNA | 144 | Homo sapiens | |
| DNA (145-mer) | J | DNA | 145 | Homo sapiens | |
| Polycomb complex protein BMI-1 | M | protein | 326 | Homo sapiens | P35226 |
| E3 ubiquitin-protein ligase RING2 | N | protein | 336 | Homo sapiens | Q99496 |
| Ubiquitin-conjugating enzyme E2 D3 | P | protein | 147 | Homo sapiens | P61077 |
| Ubiquitin | O | protein | 76 | Homo sapiens | P0CG47 |
| Ubiquitin | R | protein | 76 | Homo sapiens | P62979 |
Sequence of entity 1 (A, E), FASTA
>9V9Q_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9V9Q_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9V9Q_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>9V9Q_4 Histone H2B (chains D, H)
MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
CYTSAK
Sequence of entity 5 (I), FASTA
>9V9Q_5 DNA (144-MER) (chains I)
CGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAAC
GCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGG
CACGTGTCAGATATATACATCCGA
Sequence of entity 6 (J), FASTA
>9V9Q_6 DNA (145-MER) (chains J)
TCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTCGA
Sequence of entity 7 (M), FASTA
>9V9Q_7 Polycomb complex protein BMI-1 (chains M)
MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQV
HKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADE
DKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLR
SKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQR
DGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSP
SGNHQSSFANRPRKSSVNGSSATSSG
Sequence of entity 8 (N), FASTA
>9V9Q_8 E3 ubiquitin-protein ligase RING2 (chains N)
MSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKN
TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEY
EAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDSSHCS
NASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTLMEKD
DSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASG
QFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK
Sequence of entity 9 (P), FASTA
>9V9Q_9 Ubiquitin-conjugating enzyme E2 D3 (chains P)
MALKRINKELSDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLV
PEIARIYKTDRDKYNRISREWTQKYAM
Sequence of entity 10 (O), FASTA
>9V9Q_10 Ubiquitin (chains O)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC
Sequence of entity 11 (R), FASTA
>9V9Q_11 Ubiquitin (chains R)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Structural mechanisms of PRC1-mediated interplay between gene repression and activation. Yu, Y., Cai, D., Zhang, Y.Z. et al. To be published.
Other PDB entries of the same protein (UniProt A0A310TTQ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
- 9JNP 2.3 Å, Structure of isw1-nucleosome complex in ATP state
- 8RUP 2.42 Å, Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
- 9JNU 2.5 Å, Structure of isw1-nucleosome complex in ADP state
- 9N6H 2.54 Å, 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
- 9N6I 2.61 Å, 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex
- 9JNT 2.7 Å, Structure of isw1-nucleosome complex in ADP* state
- 9LIU 2.7 Å, Structure of isw1-nucleosome double-bound complex in ATP-ATP state
- 28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
- 9JO5 2.8 Å, Structure of isw1-nucleosome complex in ADP-B state
- 9C9X 2.83 Å, S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome
- 36IV 2.89 Å, Cryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes
Browse structure collections
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