9V9Q
Cryo-em structure of the cprc1-ubch5c e3-e2 complex bound to the h2bk120ub-modified nucleosome
PDB DOI: 10.2210/pdb9v9q/pdb
Classification: GENE REGULATION Organism(s): Homo Sapiens , Xenopus Laevis
Deposited: 2025-06-02 Deposition Author(s): Cai, D. , Huang, J. , Yu, Y. , Zhang, Y.Z.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.8 Å
Cryo-em structure of the cprc1-ubch5c e3-e2 complex bound to the h2bk120ub-modified nucleosome
Cai, D. , Huang, J. , Yu, Y. , Zhang, Y.Z.
Primary Citation of Related Structures: 9V9Q
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Histone H3 | A | 136 | Homo Sapiens , Xenopus Laevis | MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| Histone H3 | E | 136 | Homo Sapiens , Xenopus Laevis | MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| Ubiquitin | O | 76 | Homo Sapiens , Xenopus Laevis | MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC |
| Ubiquitin | R | 76 | Homo Sapiens , Xenopus Laevis | MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG |
| Histone H4 | B | 103 | Homo Sapiens , Xenopus Laevis | MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG |
| Histone H4 | F | 103 | Homo Sapiens , Xenopus Laevis | MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG |
| Histone H2A | C | 130 | Homo Sapiens , Xenopus Laevis | MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK |
| Histone H2A | G | 130 | Homo Sapiens , Xenopus Laevis | MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK |
| Histone H2B | D | 126 | Homo Sapiens , Xenopus Laevis | MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTSAK |
| Histone H2B | H | 126 | Homo Sapiens , Xenopus Laevis | MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTSAK |
| Polycomb complex protein BMI-1 | M | 326 | Homo Sapiens , Xenopus Laevis | MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQRDGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSPSGNHQSSFANRPRKSSVNGSSATSSG |
| E3 ubiquitin-protein ligase RING2 | N | 336 | Homo Sapiens , Xenopus Laevis | MSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK |
| Ubiquitin-conjugating enzyme E2 D3 | P | 147 | Homo Sapiens , Xenopus Laevis | MALKRINKELSDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| DNA (144-MER) | i | 144 | NA | CGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGA |
| DNA (145-MER) | j | 145 | NA | TCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGA |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2025-06-02 Deposition Author(s): Cai, D. , Huang, J. , Yu, Y. , Zhang, Y.Z.