2024-10-30 REL RCSB RCSB RCSB 2020-09-08 2020-10-07 2020-10-07 2024-10-30 National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) R01NS088367 United States National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) R01NS092662 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI107121 United States National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) F32NS106730 United States National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) F31NS083336 United States National Institutes of Health/National Cancer Institute (NIH/NCI) T32CA060395 United States Murine polyomavirus hexavalent capsomer, subparticle reconstruction Goetschius DJ Hafenstein SL polyomavirus, capsomer, VIRAL PROTEIN Lauver MD Goetschius DJ Netherby-Winslow CS Ayers KN Jin G Haas DG Frost EL Cho SH Bator C Bywaters SM Christensen ND Hafenstein SL Lukacher AE Antibody escape by polyomavirus capsid mutation facilitates neurovirulence. Elife US 9 2020 32940605 doi:10.7554/eLife.61056 2050-084X 7k25 FULLOVERLAP Murine polyomavirus strain A2 Murine polyomavirus strain A2 0 1 Murine polyomavirus strain A2 450.0 7 VIRION STRAIN false false Capsid protein VP1 Mus musculus polyomavirus 1 0.042493171999999996 5 Mus musculoides LEVO APKRKSGVSKCETKCTKACPRPAPVPKLLIKGGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGIN LATSDTEDSPENNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGS QYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYF GNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVKNPYP MASLISSLFNNMLPQVQGQPMEGENTQVEEVRVYDGTEPVPGDPDMTRYVDRFGKTKTVFPGN A0A247D727 singleParticle particle 2.8 7.9 10.0 HEPES 1.0 CaCl2 1.0 MgCl2 5.0 KCl
10 mM HEPES pH 7.9, 1 mM CaCl2, 1 mM MgCl2, 5 mM KCl
 ETHANE 95
MuPyV (2.8 mg/mL)
 FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 FEI FALCON III (4k x 4k) 45.0 1 Initial model generated ab initio in cryoSPARC with I1 symmetry imposed. Initial model for subvolume reconstruction was generated using 10,000 subparticles using ISECC_subpaticle_extract. 2.9 FSC 0.143 CUT-OFF RELION 3.1 929940 MAXIMUM LIKELIHOOD RELION 3.1
I1-constrained angles for whole capsid derived using 3D Refinement in RELION. Subparticle initial angles and offsets were mathematically derived from icosahedral parameters using ISECC_subpaticle_extract.
 MAXIMUM LIKELIHOOD RELION 3.1
Local search for angles and offsets in RELION from the icosahedrally-derived subparticle parameters.
 emd_22643.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 -150 -150 -150 300 300 300 330.0 330.0 330.0 90.0 90.0 90.0 X Y Z -23.310552999999999 30.466882999999999 0.000000001481236 1.0 1.1 1.1 1.1 3.0 AUTHOR Murine polyomavirus hexavalent capsomer, subparticle reconstruction 1SIE PDB experimental model 3GK8 PDB experimental model
Homology model for Fab was generated using SwissModel. Initial models were docked into density in Chimera. Fab CDR loops were manually rebuilt in Coot. Iterative rounds of real space refinements (PHENIX) and manual adjustment (coot) were conducted to improve fit to density.
REAL emd_22643_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 -150 -150 -150 300 300 300 330.0 330.0 330.0 90.0 90.0 90.0 X Y Z -0.02467346 0.052769687 0.00044729144 0.0031434936 1.1 1.1 1.1 AUTHOR Murine polyomavirus hexavalent capsomer, subparticle reconstruction emd_22643_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 -150 -150 -150 300 300 300 330.0 330.0 330.0 90.0 90.0 90.0 X Y Z -0.024211021 0.053907678 0.00044675497 0.0031440456 1.1 1.1 1.1 AUTHOR Murine polyomavirus hexavalent capsomer, subparticle reconstruction