2025-11-12 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 INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.title _em_admin.last_update PDBe PDBe 2025-04-11 2025-05-07 2025-05-07 2025-11-12 Biotechnology and Biological Sciences Research Council (BBSRC) BB/X01097X/1 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/Y005732/1 United Kingdom Satellite Tobacco Necrosis Virus-1 Saunders K Shah S Peyret H Meshcheriakova Y Richardson J Eltschkner S Lawson DM Lomonossoff G ssRNA plant virus, icosahedral, RNA packaging, VIRUS LIKE PARTICLE Saunders K Shah SN Peyret H Meshcheriakova Y Richardson J Eltschkner S Lawson DM Lomonossoff GP The Specificity of RNA Packaging in Isometric RNA Plant Viruses is Principally Determined by Replication. J.Mol.Biol. UK 437 169352 169352 2025 40706701 doi:10.1016/j.jmb.2025.169352 1089-8638 0070 JMOBAK 9qve FULLOVERLAP EMDB EMD-53395 associated EM volume
Satellite Tobacco Necrosis Virus-1
 Satellite tobacco necrosis virus 1 Satellite tobacco necrosis virus 1 0 1
The complete STNV coat protein gene was inserted into the pEff vector. Expression was initiated by infiltrating leaves of Nicotiana benthamiana with suspensions of Agrobacterium tumefaciens strain LBA4404 harbouring this vector.
Satellite tobacco necrosis virus 1 1.30 capsid 200.0 1 VIRUS-LIKE PARTICLE STRAIN false false Capsid protein Satellite tobacco necrosis virus 1 0.021739645 1 Nicotiana benthamiana LEVO MAKQQNNRRKSATMRAVKRMINTHLEHKRFALINSGNTNATAGTVQNLSNGIIQGDDINQRSGDQVRIVSHKLHVRGTAI TVSQTFRFIWFRDNMNRGTTPTVLEVLNTANFMSQYNPITLQQKRFTILKDVTLNCSLTGESIKDRIINLPGQLVNYNGA TAVAASNGPGAIFMLQIGDSLVGLWDSSYEAVYTDA P03606 MAGNESIUM ION 2.4305e-05 3 MG singleParticle particle 2.92 7.4
1 x phosphate-buffered saline
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE
glow discharged for 60 seconds at 8 mA using an ACE 200 (Leica Microsystems)
 ETHANE 100 277 FEI VITROBOT MARK IV TFS TALOS F200C FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.7000000000000001 1.8 150000.0 GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN TFS FALCON 4i (4k x 4k) 4096 4096 1 2703 2.85 30.0
The particles were densely packed showing mostly 5-fold views
 TFS FALCON 4i (4k x 4k) 4096 4096 1 575 2.82 30.0
Regions with a lower particle density were selected, giving additional views, but still dominated by 5-folds.
 TFS FALCON 4i (4k x 4k) 4096 4096 1 985 3.49 40.0
Data were collected with a positive 20 degree tilt giving a better distribution of views.
 1 2394377
combined figure from the 3 datasets
 cryoSPARC 4.5.3 PHASE FLIPPING AND AMPLITUDE CORRECTION 2BUK 1 I FOURIER SPACE 2.77 FSC 0.143 CUT-OFF cryoSPARC 4.5.3 207142 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 4 cryoSPARC 4.5.3 emd_53395.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 470.0 470.0 470.0 90.0 90.0 90.0 X Y Z -0.75441986 1.3217201 -0.00062968663 0.043324903 0.94 0.94 0.94 0.3 AUTHOR Sharpened map at 2.77 A resolution used for model building and refinement 2BUK PDB experimental model FLEXIBLE FIT cross-correlation coefficient REAL 43.0 emd_53395_msk_1.map emd_53395_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 470.0 470.0 470.0 90.0 90.0 90.0 X Y Z -0.13094422 0.34146535 -0.00062968663 0.0152561255 0.94 0.94 0.94 AUTHOR Unsharpened map emd_53395_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 470.0 470.0 470.0 90.0 90.0 90.0 X Y Z -0.16109699 0.36752322 0.00013428586 0.02164814 0.94 0.94 0.94 AUTHOR Half map 2 emd_53395_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 470.0 470.0 470.0 90.0 90.0 90.0 X Y Z -0.15987879 0.34205824 0.00013556136 0.021738848 0.94 0.94 0.94 AUTHOR Half map 1