8U5H
Cryo-em structure of human dnmt3a udr bound to h2ak119ub1-modified nucleosome
PDB DOI: 10.2210/pdb8u5h/pdb
Classification: STRUCTURAL PROTEIN/TRANSFERASE/DNA Organism(s): Homo Sapiens , Xenopus Laevis
Deposited: 2023-09-12 Deposition Author(s): Chen, X. , Song, J.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.23 Å
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| DNA (cytosine-5)-methyltransferase 3A | A | 98 | Homo Sapiens , Xenopus Laevis | PEASRAVENGCCTPKEGRGAPAEAGKEQKETNIESMKMEGSRGRLRGGLGWESSLRQRPMPRLTFQAGDPYYISKRKRDEWLARWKREAEKKAKVIAG |
| DNA (cytosine-5)-methyltransferase 3A | B | 98 | Homo Sapiens , Xenopus Laevis | PEASRAVENGCCTPKEGRGAPAEAGKEQKETNIESMKMEGSRGRLRGGLGWESSLRQRPMPRLTFQAGDPYYISKRKRDEWLARWKREAEKKAKVIAG |
| Ubiquitin | D | 76 | Homo Sapiens , Xenopus Laevis | MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG |
| Histone H3.3C | I | 136 | Homo Sapiens , Xenopus Laevis | MARTKQTARKSTGGKAPRKQLVTKAAKKCAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQRSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| Histone H3.3C | O | 136 | Homo Sapiens , Xenopus Laevis | MARTKQTARKSTGGKAPRKQLVTKAAKKCAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQRSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| Histone H4 | J | 103 | Homo Sapiens , Xenopus Laevis | MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG |
| Histone H4 | Q | 103 | Homo Sapiens , Xenopus Laevis | MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG |
| Histone H2A | K | 130 | Homo Sapiens , Xenopus Laevis | MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKCTESSKSAKSK |
| Histone H2A | R | 130 | Homo Sapiens , Xenopus Laevis | MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKCTESSKSAKSK |
| Histone H2B 1.1 | M | 123 | Homo Sapiens , Xenopus Laevis | MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK |
| Histone H2B 1.1 | S | 123 | Homo Sapiens , Xenopus Laevis | MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| nucleosome DNA | c | 180 | NA | GCTCTCTACGTAAACATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGACTTACCCACTTCG |
| nucleosome DNA | h | 180 | NA | CGAAGTGGGTAAGTCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGATGTTTACGTAGAGAGC |
Experimental Data
Method: ELECTRON MICROSCOPY