Structure of the Retron IA Complex without the HNH Nuclease

2025-11-12 REL RCSB INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Polymer geometry

The modelling of residues 76 and 77 in chain H (msDNA) were improved to better fit the density and engage in base-pairing interactions with A13 and A14, respectively.

STRUCTURE_SUMMARY atom_site citation citation_author em_admin em_software entity entity_poly entity_poly_seq entity_src_gen ndb_struct_conf_na ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_contact_author pdbx_poly_seq_scheme pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_residues pdbx_validate_rmsd_angle pdbx_validate_torsion refine_ls_restr struct_conf struct_conn struct_ref struct_ref_seq struct_sheet_range _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.label_seq_id _em_admin.last_update _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.seq_align_end _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_seq_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_seq_id RCSB RCSB 2025-02-05 2025-04-23 2025-04-23 2025-11-12 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 5F31GM153146-02 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1R35GM134867 United States Structure of the Retron IA Complex without the HNH Nuclease Burman N Thomas-George J Wilkinson R Wiedenheft B Retron, IA, Immune, Transferase-DNA-RNA complex George JT Burman N Wilkinson RA de Silva S McKelvey-Pham Q Buyukyoruk M Dale A Landman H Graham AB DeLuca SZ Wiedenheft B Structural basis of antiphage defence by an ATPase-associated reverse transcriptase. Nat Commun UK 16 8459 8459 2025 41006229 doi:10.1038/s41467-025-63285-6 2041-1723 George JT Burman N Wilkinson RA de Silva S McKelvey-Pham Q Buyukyoruk M Dale A Landman H Graham A DeLuca SZ Wiedenheft B Structural basis of antiphage defense by an ATPase-associated reverse transcriptase. Biorxiv US 2025 40196496 doi:10.1101/2025.03.26.645336 2692-8205 9n6c FULLOVERLAP EMDB EMD-49056 associated EM volume

Retron IA surveillance complex with HNH nuclease bound in the "down" orientation Retron IA surveillance complex with HNH nuclease bound in the "down" orientation 0 1 2 3 4 Escherichia coli FORC_082 AAA family ATPase Escherichia coli FORC_082 0.063393953 4 Escherichia coli BL21 LEVO MWSHPQFEKINKMNLETCYVDFLELESHVINEDYLKESVELQKLISTLNESKFHLNKIGIHDFKRIRELQISLEDDLTVF VGDNGFGKSTILDAIAIVLSWLRSNIEKESKPGTYIKSHEVNNSVDVEYASIDANIKLKDFNTSILITKAKEGAYYSRNN ELLGVKKLASIYRLVNKYVDNASLPLMAYYSIARSYIGGGVDRKRKNAKTKTVWSKFDVYDEIEFDRNDFTDFFQWLVFL HNRASQEKLSESQTTINALFSDIQSLKATLTQLSAIDNIDSTVIKGLELSLKEKLNYMKSLQSGEHKFNNAVSLYDSVIN TILKFLPEFQWIKLVYGDDDYKIILKKGEVELDIQQLSQGEKTIFTLVGDLARRLILLNPNLSNPLLGYGIVLIDEIDLH LHPQWQQTIIERLTSTFPNVQFVITTHSPQVLSTVSSRSVRILQEVEVDGVNDLIVSHPDYQIKGVSNQDALLYGMRTDP IPSTKENGWLEEYKKLVELNRYSSDEALLLREKVIKHFGLDHPLVQECDDLISVLEFKNKINQHFSGSKDVK A0AAD2V6K7 RNA-directed DNA polymerase Escherichia coli 0.036046191 1 Escherichia coli BL21 LEVO MQLTSKIISKFNYNRLAFQLLLNEAPKKYKVYYIPKRGAGFRVIAQPTKELKNVQRFIVSLLQPKLPVHHKAMAYEYKKS IKDNALLHKDNNYILKMDFQNFFNKIKPDIFFSKLENTGLKLDSFDENTLRNLLFWRPGKKRSTTLILSVGAPSSPFISN FVMYDFDKSLDDWCRNNGITYSRYADDITFSTNIKDILCRVPKVVKKMLSLHVPGLSINESKTIFTSMAHNRHVTGVTLT PQGNLSIGRDRKRMLFAKIHKYSLGLLSSEEINKTKGMIAFANYLEGDFLLRLQKKYGCELITKFLMEGNK A0AAD2V6H6 2.7.7.49 Retron IA msDNA Escherichia coli FORC_082 0.028334156 1 (DT)(DA)(DA)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DA)(DA)(DA)(DG)(DA)(DC)(DA)(DC)(DA) (DG)(DA)(DT)(DT)(DT)(DC)(DT)(DC)(DC)(DT)(DT)(DC)(DG)(DC)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DC)(DC)(DC)(DC)(DG)(DG)(DG)(DC)(DA)(DG)(DG)(DG)(DA)(DT)(DG)(DC)(DG)(DA)(DA) (DG)(DG)(DA)(DG)(DA)(DA)(DA)(DT)(DC)(DT)(DG)(DT)(DG)(DT)(DC)(DT)(DT)(DT)(DC)(DG) (DC)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DA)(DC)(DC) CP026641.1 DNA Retron IA ncRNA Escherichia coli FORC_082 0.020258928 1 UAGUGUAGGAACAUUGGUUCCAGCCGGGUGAUUAGCCAGGCUUAAAUUUAUUGUCCGGUUUAG CP026641.1 ADENOSINE-5'-TRIPHOSPHATE 0.000507181 3 ATP singleParticle particle 7.5 C-flat-1.2/1.3 COPPER 300 CARBON HOLEY ARRAY GLOW DISCHARGE 45 AIR ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 2.5 45000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 13695 56.69 1 5915380

Particles picked using a 20 Angstrom lowpass filtered template volume that was produced de novo using blob picked particles

PHASE FLIPPING AND AMPLITUDE CORRECTION 1 C1 FOURIER SPACE 2.99 FSC 0.143 CUT-OFF

Reported resolution from cryoSPARC's GSFSC estimation

513948 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 3 414987.0

Focused 3-D Classification was used to parse particle stacks based on HNH occupancy and orientation

emd_49056.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 434.92798 434.92798 434.92798 90.0 90.0 90.0 X Y Z -0.10702835 0.28486577 -0.000009570875 0.0043392135 0.9061 0.9061 0.9061 0.015 AUTHOR ::::EMDATABANK.org::::EMD-49056:::: Structure of the Retron IA Complex without the HNH Nuclease AlphaFold in silico model

The structure of each subunit was predicted individually in Alphafold before rigid body fitting in ChimeraX

RIGID BODY FIT

Alphafold predicted structures of each individual subunit were first rigid body fit in ChimeraX using the fit in map command before initial relaxation using ISOLDE and final refinement in PHENIX RealSpaceRefinement. COOT was used for manual editing.

Cross-correlation coefficient REAL emd_49056_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 434.92798 434.92798 434.92798 90.0 90.0 90.0 X Y Z -0.42901877 0.45541003 0.00004029307 0.026266849 0.9061 0.9061 0.9061 AUTHOR ::::EMDATABANK.org::::EMD-49056:::: Half Map A emd_49056_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 434.92798 434.92798 434.92798 90.0 90.0 90.0 X Y Z -0.37951615 0.45859036 0.000040279207 0.026293794 0.9061 0.9061 0.9061 AUTHOR ::::EMDATABANK.org::::EMD-49056:::: Half Map B