Cryo-EM structure of the Retron-Eco7 complex (state 1)

2025-12-17 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBj PDBj 2024-11-12 2025-11-12 2025-11-12 2025-12-17 Japan Society for the Promotion of Science (JSPS) 23KJ0720 Japan Japan Society for the Promotion of Science (JSPS) 21H05281 Japan Japan Society for the Promotion of Science (JSPS) 22H00403 Japan Cryo-EM structure of the Retron-Eco7 complex (state 1) Ishikawa J Yoneyama K Yamashita K Nishimasu H Nishimasu H Retron, Reverse transcriptase, RNA BINDING PROTEIN Ishikawa J Yoneyama K Azam AH Nagao A Mitsuda Y Nakazaki R Chihara K Hiraizumi M Yamashita K Suzuki T Kiga K Nishimasu H Structural mechanism of the Retron-Eco7 anti-phage defense system. Nat Commun UK 16 10821 10821 2025 41330933 doi:10.1038/s41467-025-66589-9 2041-1723 9kjx FULLOVERLAP EMDB EMD-62378 associated EM volume

Retron-Eco7 complex (state 1) Retron-Eco7 complex (state 1) 0 1 2 3 4 5 Escherichia coli RNA-directed DNA polymerase Escherichia coli 0.036682362999999996 1 Escherichia coli LEVO MGHHHHHHGGGSSVIRGLAAVLRQSDSDISAFLVTAPRKYKVYKIPKRTTGFRVIAQPAKGLKDIQRAFVQLYSLPVHDA SMAYMKGKGIRDNAAAHAGNQYLLKADLEDFFNSITPAIFWRCIEMSSAQTPQFEPQDKLFIEKILFWQPIKRRKTKLIL SVGAPSSPVISNFCMYEFDNRIHAACKKVEITYTRYADDLTFSSNIPDVLKAVPSTLEVLLKDLFGSALRLNHSKTVFSS KAHNRHVTGITINNEETLSLGRDRKRFIKHLINQYKYGLLDNEDKAYLIGLLAFASHIEPSFITRMNEKYSLELMERLRG QR 2.7.7.49 AAA family ATPase Escherichia coli 0.062467766 4 Escherichia coli LEVO MTKQYERKAKGGNLLSAFELYQRNSDKAPGLGEMLVGEWFEMCRDYIQDGHVDESGIFRPDNAFYLRRLTLKDFRRFSLL EIKLEEDLTVIIGNNGKGKTSILYAIAKTLSWFVANILKEGGSGQRLSEMTDIKNDAEDRYSDVSSTFFFGKGLKSVPIR LSRSALGTAERRDSEVKPAKDLADIWRVINEVNTINLPTFALYNVERSQPFNRNIKDNTGRREERFDAYSQTLGGAGRFD HFVEWYIYLHKRTVSDISSSIKELEQQVNDLQRTVDGGMVSVKSLLEQMKFKLSEAIERNDAAVSSRVLTESVQKSIVEK AICSVVPSISNIWVEMITGSDLVKVTNDGHDVTIDQLSDGQRVFLSLVADLARRMVMLNPLLENPLEGRGIVLIDEIELH LHPKWQQEVILNLRSAFPNIQFIITTHSPIVLSTIEKRCIREFEPNDDGDQSFLDSPDMQTKGSENAQILEQVMNVHSTP PGIAESHWLGNFELLLLDNSGELDNHSQVLYDQIKAHFGIDSIELKKADSLIRINKMKNKLNKIRAEKGK A0AAW7FAT4 TIGR02646 family protein Escherichia coli 0.029739085999999998 2 Escherichia coli LEVO MRELARLERPEILDQYIAGQNDWMEIDQSAVWPKLTEMQGGFCAYCECRLNRCHIEHFRPRGKFPALTFIWNNLFGSCGD SRKSGGWSRCGIYKDNGAGAYNADDLIKPDEENPDDYLLFLTTGEVVPAIGLTGRALKKAQETIRVFNLNGDIKLFGSRR TAVQAIMPNVEYLYTLLEEFDEDDWNEMLRDELEKIESDEYKTALKHAWTFNQEFAGGGSGGGSSSGLVPRGSHMASWSH PQFEKGGGSGGGSGGSAWSHPQFEKN msrRNA Escherichia coli 0.046843565999999996 1 GGACUCUUUAGCGUUGGACGGUUACGUCUAGUCGGGUGAUUAGCCAGACUCUAACUUAUUGAACGUAUUAAGGGUUGCGA AAGUGUCGCAACCCGAGAUCGUUCCUCUCUCGGGUUGCGACACUUUCGCUUCCUCAAGUAAAGAGU msdDNA Escherichia coli 0.023807241999999996 1 (DT)(DT)(DG)(DA)(DG)(DG)(DA)(DA)(DG)(DC)(DG)(DA)(DA)(DA)(DG)(DT)(DG)(DT)(DC)(DG) (DC)(DA)(DA)(DC)(DC)(DC)(DG)(DA)(DG)(DA)(DG)(DA)(DG)(DG)(DA)(DA)(DC)(DG)(DA)(DT) (DC)(DT)(DC)(DG)(DG)(DG)(DT)(DT)(DG)(DC)(DG)(DA)(DC)(DA)(DC)(DT)(DT)(DT)(DC)(DG) (DC)(DA)(DA)(DC)(DC)(DC)(DT)(DT)(DA)(DA)(DT)(DA)(DC)(DG)(DT)(DT)(DC) U02551.1 DNA ADENOSINE-5'-DIPHOSPHATE 0.000427201 3 ADP ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 7.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.0 GATAN K3 BIOQUANTUM (6k x 4k) 49.7 1 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION C1 2.76 FSC 0.143 CUT-OFF cryoSPARC 67250 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_62378.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 398.4 398.4 398.4 90.0 90.0 90.0 X Y Z -0.5667909 1.0030968 -0.00006872833 0.019139314 0.996 0.996 0.996 0.1 AUTHOR ::::EMDATABANK.org::::EMD-62378:::: emd_62378_msk_1.map emd_62378_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 398.4 398.4 398.4 90.0 90.0 90.0 X Y Z -0.19656527 0.45439187 0.00011398411 0.020206379 0.996 0.996 0.996 AUTHOR ::::EMDATABANK.org::::EMD-62378:::: emd_62378_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 398.4 398.4 398.4 90.0 90.0 90.0 X Y Z -0.17753464 0.44775778 0.00010370793 0.020230262 0.996 0.996 0.996 AUTHOR ::::EMDATABANK.org::::EMD-62378::::