Cryo-em structure of ddm1-nucleosome complex
PDB DOI: 10.2210/pdb8j90/pdb
Classification: NUCLEAR PROTEIN Organism(s): Arabidopsis Thaliana , Synthetic Construct
Deposited: 2023-05-02 Deposition Author(s): Berger, F. , Hatazawa, S. , Horikoshi, N. , Kakutani, T. , Kurumizaka, H. , Osakabe, A. , Takizawa, Y.
Method: ELECTRON MICROSCOPY Resolution: 4.71 Å
Cryo-em structure of ddm1-nucleosome complex
Berger, F. , Hatazawa, S. , Horikoshi, N. , Kakutani, T. , Kurumizaka, H. , Osakabe, A. , Takizawa, Y.
Primary Citation of Related Structures: 8J90
Proteins | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Sequence |
Histone H3.1 | A | 139 | Arabidopsis Thaliana , Synthetic Construct | GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
Histone H3.1 | E | 139 | Arabidopsis Thaliana , Synthetic Construct | GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
Histone H4 | B | 106 | Arabidopsis Thaliana , Synthetic Construct | GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG |
Histone H4 | F | 106 | Arabidopsis Thaliana , Synthetic Construct | GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG |
HTA6 | C | 153 | Arabidopsis Thaliana , Synthetic Construct | GSHMESTGKVKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGAPVYMAAVLEYLAAEVLELAGNAARDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGGVLPNINSVLLPKKSATKPAEEKATKSPVKSPKKA |
HTA6 | G | 153 | Arabidopsis Thaliana , Synthetic Construct | GSHMESTGKVKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGAPVYMAAVLEYLAAEVLELAGNAARDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGGVLPNINSVLLPKKSATKPAEEKATKSPVKSPKKA |
HTB9 | D | 153 | Arabidopsis Thaliana , Synthetic Construct | GSHMAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS |
HTB9 | H | 153 | Arabidopsis Thaliana , Synthetic Construct | GSHMAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS |
ATP-dependent DNA helicase DDM1 | K | 767 | Arabidopsis Thaliana , Synthetic Construct | GPHMVSLRSRKVIPASEMVSDGKTEKDASGDSPTSVLNEEENCEEKSVTVVEEEILLAKNGDSSLISEAMAQEEEQLLKLREDEEKANNAGSAVAPNLNETQFTKLDELLTQTQLYSEFLLEKMEDITINGIESESQKAEPEKTGRGRKRKAASQYNNTKAKRAVAAMISRSKEDGETINSDLTEEETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIGFLSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYHGDKNQRDELRRKHMPKTVGPKFPIVITSYEVAMNDAKRILRHYPWKYVVIDEGHRLKNHKCKLLRELKHLKMDNKLLLTGTPLQNNLSELWSLLNFILPDIFTSHDEFESWFDFSEKNKNEATKEEEEKRRAQVVSKLHGILRPFILRRMKCDVELSLPRKKEIIMYATMTDHQKKFQEHLVNNTLEAHLGENAIRGQGWKGKLNNLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQCGKFRLLERLLVRLFANNHKVLIFSQWTKLLDIMDYYFSEKGFEVCRIDGSVKLDERRRQIKDFSDEKSSCSIFLLSTRAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETRVLKRAYSKLKLEHVVIGQGQFHQERAKSSTPLEEEDILALLKEDETAEDKLIQTDISDADLDRLLDRSDLTITAPGETQAAEAFPVKGPGWEVVLPSSGGMLSSLNS |
Nucleic Acids / Hybrid | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Sequence |
DNA (169-MER) | i | 169 | NA | ATCGGACCCTATCGCGAGCCAGGCCTGAGAATCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT |
DNA (169-MER) | j | 169 | NA | ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGATTCTCAGGCCTGGCTCGCGATAGGGTCCGAT |
Method: ELECTRON MICROSCOPY
Deposited Date: 2023-05-02 Deposition Author(s): Berger, F. , Hatazawa, S. , Horikoshi, N. , Kakutani, T. , Kurumizaka, H. , Osakabe, A. , Takizawa, Y.