Cryo-EM structure of activated retron Eco2 (Ec67)

2026-03-04 REL PDBe 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.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_PubMed _citation.title _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_PubMed _citation.title _citation_author.name _em_admin.last_update PDBe PDBe 2025-07-18 2026-02-18 2026-02-18 2026-03-04 European Molecular Biology Organization (EMBO) 5342-2023 European Union Cryo-EM structure of activated retron Eco2 (Ec67) Skorupskaite A Jasnauskaite M Grigaitis R Malinauskaite L Pausch P Retron, Reverse transcriptase, DNA, RNA, TOPRIM, RNaseH, msDNA, ANTIVIRAL PROTEIN Jasnauskaite M Juozapaitis J Liegute T Grigaitis R Skorupskaite A Steinchen W Miksys A Truncaite L Kazlauskaite K Torres Jimenez MF Khochare S Dudas G Bange G Malinauskaite L Songailiene I Pausch P Structure and mechanism of antiphage retron Eco2. Nat.Struct.Mol.Biol. US 33 330 340 2026 41709047 doi:10.1038/s41594-026-01754-2 1545-9985 9s1f FULLOVERLAP PDB 9I2G unspecified PDB 9I2F unspecified EMDB EMD-54448 associated EM volume

Ternary complex of activated retron Eco2 (Ec67) with RNA and DNA Ternary complex of activated retron Eco2 (Ec67) with RNA and DNA 0 1 2 3 Escherichia coli NCTC 86 23 RNA (132-MER) Escherichia coli NCTC 86 23 0.042593202999999996 3 CACGCAUGUAGGCAGAUUUGUUGGUUGUGAAUCGCAACCAGUGGCCUUAAUGGCAGGAGGAAUCGCCUCCCUAAAAUCCU UGAUUCAGAGCUAUACGGCAGGUGUGCUGUGCGAAGGAGUGCCUGCAUGCGU Retron Ec67 protein Escherichia coli NCTC 86 23 0.068511922 3 Escherichia coli DH5[alpha] LEVO MTKTSKLDALRAATSREDLAKILDVKLVFLTNVLYRIGSDNQYTQFTIPKKGKGVRTISAPTDRLKDIQRRICDLLSDCR DEIFAIRKISNNYSFGFERGKSIILNAYKHRGKQIILNIDLKDFFESFNFGRVRGYFLSNQDFLLNPVVATTLAKAACYN GTLPQGSPCSPIISNLICNIMDMRLAKLAKKYGCTYSRYADDITISTNKNTFPLEMATVQPEGVVLGKVLVKEIENSGFE INDSKTRLTYKTSRQEVTGLTVNRIVNIDRCYYKKTRALAHALYRTGEYKVPDENGVLVSGGLDKLEGMFGFIDQVDKFN NIKKKLNKQPDRYVLTNATLHGFKLKLNAREKAYSKFIYYKFFHGNTCPTIITEGKTDRIYLKAALHSLETSYPELFREK TDSKKKEINLNIFKSNEKTKYFLDLSGGTADLKKFVERYKNNYASYYGSVPKQPVIMVLDNDTGPSDLLNFLRNKVKSCP DDVTEMRKMKYIHVFYNLYIVLTPLSPSGEQTSMEDLFPKDILDIKIDGKKFNKNNDGDSKTEYGKHIFSMRVVRDKKRK IDFKAFCCIFDAIKDIKEHYKLMLNSGSWSHPQFEK P21325 2.7.7.49 msDNA (67-MER) Escherichia coli NCTC 86 23 0.020522113 3 (DT)(DC)(DC)(DT)(DT)(DC)(DG)(DC)(DA)(DC)(DA)(DG)(DC)(DA)(DC)(DA)(DC)(DC)(DT)(DG) (DC)(DC)(DG)(DT)(DA)(DT)(DA)(DG)(DC)(DT)(DC)(DT)(DG)(DA)(DA)(DT)(DC)(DA)(DA)(DG) (DG)(DA)(DT)(DT)(DT)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DG)(DC)(DG)(DA)(DT)(DT)(DC)(DC) (DT)(DC)(DC)(DT)(DG)(DC)(DC) DNA MAGNESIUM ION 2.4305e-05 7 MG singleParticle particle 2 8.0 50.0 Tris-HCl 150.0 NaCl 10.0 MgCl2 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 20.0 GLOW DISCHARGE 7 AIR

20 mA

ETHANE 100 277.15 FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.0 1.0 2.0 2.0 92000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN EPU 3.10 FEI FALCON III (4k x 4k) COUNTING 4096 4096 1 2968 46.33 29.0 1 2271864

Template picking

PHASE FLIPPING AND AMPLITUDE CORRECTION AlphaFold C1 2.9 FSC 0.143 CUT-OFF cryoSPARC 4.7

Symmetry expanded particles were used

617364 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_54448.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.46908766 0.90183365 -0.0010151684 0.018021906 1.1 1.1 1.1 0.08 AUTHOR ::::EMDATABANK.org::::EMD-54448:::: Sharp map used for refinements AlphaFold in silico model D_1292144007 Other experimental model

Model from another deposition

emd_54448_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.20364507 0.472756 -0.0013570586 0.01300596 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-54448:::: volume map emd_54448_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.19696729 0.5102037 -0.00011175517 0.014536407 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-54448:::: emd_54448_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.22210935 0.49623147 -0.00012072965 0.014560546 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-54448::::