2024-07-24 REL PDBe PDBe PDBe 2022-12-19 2023-04-05 2023-04-05 2024-07-24 European Research Council (ERC) 741863 European Union Swiss National Science Foundation 200020_159707 Switzerland Swiss National Science Foundation 200020_188711 Switzerland African cichlid nackednavirus capsid at pH 5.5 Pfister S Rabl J Boehringer D Meier BH T=3, Capsid protein, VIRAL PROTEIN Pfister S Rabl J Wiegand T Mattei S Malar AA Lecoq L Seitz S Bartenschlager R Bockmann A Nassal M Boehringer D Meier BH Structural conservation of HBV-like capsid proteins over hundreds of millions of years despite the shift from non-enveloped to enveloped life-style. Nat Commun UK 14 1574 1574 2023 36949039 doi:10.1038/s41467-023-37068-w 2041-1723 8c0o FULLOVERLAP African cichlid nackednavirus African cichlid nackednavirus 0 1 African cichlid nackednavirus Ophthalmotilapia ventralis 3.57 capsid 230.0 3 VIRUS-LIKE PARTICLE OTHER false false C protein African cichlid nackednavirus 0.019851234 180 Escherichia coli LEVO MGTFIELVKNMKGYKELLLPMEMVPLPAVVLKHVKLILTSQKEHQPWMTEMALKADQCLIHKATLDLAGKATSNEAKPLI EAMQQIILAMTRELWGQIQRHHYGIVQVEHYVKQITLWQDTPQAFRGDQPKPPSFRSDGPTRGQGSFRPFFRGRGRGRGR GRGSQSPARKGPLPK A0A3S9H6T3 singleParticle particle 5.5 50.0 acetate sodium acetate 50.0 NaCl Sodium chloride 5.0 EDTA EDTA 5.0 DTT DTT Quantifoil R2/2 COPPER 300 CARBON CONTINUOUS 1.0 GLOW DISCHARGE ETHANE-PROPANE 100 277 FEI VITROBOT MARK IV
The protein concentration is approx. 0.1-0.5 mg/mL
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.5 0.5 2.0 2.0 166000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 FEI FALCON III (4k x 4k) INTEGRATING 1-40 5362 55.0 1 215225
Map of African cichlid nackednavirus capsid at pH 7.5
 1 I 3.9 FSC 0.143 CUT-OFF RELION 3.1 77129 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 10 RELION 3.1 emd_16371.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 362.87997 362.87997 362.87997 90.0 90.0 90.0 X Y Z -0.032989837 0.050880015 0.00017846256 0.0030670583 0.8399999 0.8399999 0.8399999 0.009 AUTHOR Refined sharpened map of recombinant African Cichlid Nackednavirus capsid at pH 5.5 AB INITIO MODEL
One protein chain was manually built in Coot. The chain was multiplied to give 180 chains, which were arranged as an icosahedral capsid. The capsid was refined with phenix and Isolde.
REAL emd_16371_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 362.87997 362.87997 362.87997 90.0 90.0 90.0 X Y Z -0.0048143184 0.013686771 0.00019419233 0.001507286 0.8399999 0.8399999 0.8399999 AUTHOR Half map of recombinant African Cichlid Nackednavirus capsid at pH 5.5 emd_16371_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 362.87997 362.87997 362.87997 90.0 90.0 90.0 X Y Z -0.0047980705 0.013837758 0.00019422866 0.0015120059 0.8399999 0.8399999 0.8399999 AUTHOR Half map of recombinant African Cichlid Nackednavirus capsid at pH 5.5