Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer with endonuclease domain density

2026-03-18 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation 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 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 RCSB RCSB 2025-07-22 2026-02-25 2026-02-25 2026-03-18 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P30AI045008 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM108751 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) T32AI007632 United States Department of Health & Human Services (HHS) S10OD018483 United States National Science Foundation (NSF, United States) DMR2342336 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1P30GM124166 United States Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer with endonuclease domain density Montermoso S Gupta K Pumroy RA Moiseenkova-Bell V Bushman FD Van Duyne GD SF3 helicase, DNA binding protein, Replication, Viral protein Montermoso S Gupta K Pumroy RA Moiseenkova-Bell V Bushman FD Van Duyne GD Structures of nucleotide-bound Redondovirus Rep protein link conformation and function. Plos Pathog. US 22 e1013997 e1013997 2026 41779823 doi:10.1371/journal.ppat.1013997 1553-7374 EMD-71784 other EM volume 9pqm FULLOVERLAP EMDB EMD-71784 other EM volume EMDB EMD-71786 associated EM volume

PDB 9PQJ unspecified PDB 9PQF unspecified ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density 0 1 Vientovirus FB 0.243 Replication-associated protein Human lung-associated vientovirus FB 0.024360986 6 Escherichia coli BL21(DE3) LEVO EKREKAELMINGNLRELFMEGVLGAIDIIRAEKLRNIFQVQAPADKYQKKLILWFKGETGEGKTKTAVDIAERFFNGEYW MSNETLKWFDGYRGQPVAIIDDFRKSMLTEWSFLLRLLDGYNLIVQVKGGFVKWQPKVIIVTSPASPSEAFQWVNKEGEI IEWDKQVQLTRRLTYEDEEQIYNFPLWNQDQLKLENTIRKYLGLAPM A0A4D6K5Y8 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER 0.0005232469999999999 6 AGS MAGNESIUM ION 2.4305e-05 6 MG singleParticle particle 0.2 7.5 20.0 HEPES 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid 300.0 NaCl sodium chloride 0.1 TCEP tris(2-carboxyethyl)phosphine 2.5 C3H8O3 glycerol 5.0 MgCl2 magnesium chloride 5.0 C10H16N5O12P3S Adenosine 5'-O-(3-thiotriphosphate

20 mM HEPES-NaOH pH 7.5, 300 mM NaCl, 0.1 mM TCEP, 2.5% glycerol added with 5 mM MgCl2 and 5mM ATPgammaS

Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE 30 AIR 0.03 ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 3.0 GATAN K3 (6k x 4k) 1 5605 1.42 41.3 1 5286720 cryoSPARC 4.5.3 Patch CTF estimation RELION 5.0-beta CTFFind-4.1.14 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 3.18 FSC 0.143 CUT-OFF RELION 5.0-beta 75338 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 nonuniform refinement MAXIMUM LIKELIHOOD RELION 5.0-beta 3D auto-refinement 6 RELION 5.0-beta emd_71786.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 241.92 241.92 241.92 90.0 90.0 90.0 Z Y X -17.450168999999999 33.184109999999997 -0.000000000000773 1.0 0.84 0.84 0.84 4.4 AUTHOR ::::EMDATABANK.org::::EMD-71786:::: sharpened map of 3D auto-refined map from Relion (primary map) 9PQJ 121-327 PDB experimental model RIGID BODY FIT

Initial rigid body fitting was done in ChimeraX followed by flexible fitting in coot

REAL 80.790000000000006 emd_71786_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 241.92 241.92 241.92 90.0 90.0 90.0 X Y Z -0.0084025655 0.024263246 0.000033443397 0.00083453336 0.84 0.84 0.84 AUTHOR ::::EMDATABANK.org::::EMD-71786:::: 3D auto-refined map from Relion emd_71786_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 241.92 241.92 241.92 90.0 90.0 90.0 X Y Z -0.01433917 0.030349059 0.000030986495 0.0012089104 0.84 0.84 0.84 AUTHOR ::::EMDATABANK.org::::EMD-71786:::: half map 2 from 3D auto-refinement in Relion emd_71786_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 241.92 241.92 241.92 90.0 90.0 90.0 X Y Z -0.020577079 0.03605892 0.000038601473 0.0020346725 0.84 0.84 0.84 AUTHOR ::::EMDATABANK.org::::EMD-71786:::: half map 1 from 3D auto-refinement in Relion