2024-07-24 REL PDBe PDBe PDBe 2022-07-01 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 7.5 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 8aac 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 BL21(DE3) LEVO MGTFIELVKNMKGYKELLLPMEMVPLPAVVLKHVKLILTSQKEHQPWMTEMALKADQCLIHKATLDLAGKATSNEAKPLI EAMQQIILAMTRELWGQIQRHHYGIVQVEHYVKQITLWQDTPQAFRGDQPKPPSFRSDGPTRGQGSFRPFFRGRGRGRGR GRGSQSPARKGPLPK A0A3S9H6T3 singleParticle particle 7.5 50.0 TRIS-HCl TRIS-HCl 50.0 NaCl Sodium chloride 5.0 EDTA EDTA 5.0 DTT DTT Quantifoil COPPER 300 CARBON CONTINUOUS 1.0 GLOW DISCHARGE
15 mA
 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 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K2 QUANTUM (4k x 4k) COUNTING 1-40 8999 76.0 1 375654
relion stochastic gradient descent
 I FOURIER SPACE 3.7 FSC 0.143 CUT-OFF RELION 3.1 70868 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 10 RELION 3.1 emd_15295.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 462.24002 462.24002 462.24002 90.0 90.0 90.0 X Y Z -0.019340305 0.042958472 0.00033896195 0.002057049 1.07 1.07 1.07 0.0103 AUTHOR ACNDV capsid at pH 7.5 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_15295_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 462.24002 462.24002 462.24002 90.0 90.0 90.0 X Y Z -0.057267748 0.108744584 0.0000045702805 0.000567014 1.07 1.07 1.07 AUTHOR Map obtained by symmetry expansion showing only the three chains of the asymmetric unit emd_15295_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 462.24002 462.24002 462.24002 90.0 90.0 90.0 X Y Z -0.056563348 0.10915734 0.000008322134 0.000771537 1.07 1.07 1.07 AUTHOR Map obtained by symmetry expansion emd_15295_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 462.24002 462.24002 462.24002 90.0 90.0 90.0 X Y Z -0.0047216984 0.016341427 0.00026586204 0.0016723927 1.07 1.07 1.07 AUTHOR ACNDV capsid at pH 7.5, unfiltered half map 1 emd_15295_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 462.24002 462.24002 462.24002 90.0 90.0 90.0 X Y Z -0.0038043542 0.01608895 0.00026597007 0.0016708262 1.07 1.07 1.07 AUTHOR ACNDV capsid at pH 7.5, unfiltered half map 2