2024-05-22 REL PDBe PDBe PDBe 2022-06-16 2023-12-20 2023-12-20 2024-05-22 German Federal Ministry for Education and Research 03Z22HN23 Germany German Federal Ministry for Education and Research 03Z22HI2 Germany German Federal Ministry for Education and Research 03COV04 Germany German Research Foundation (DFG) 391498659 Germany European Regional Development Fund EFRE: ZS/2016/04/78115 European Union Capsid structure of the L-A helper virus from native viral communities Schmidt L Tueting C Kyrilis F Hamdi F Semchonok DA Kastritis PL Capsid structure ScVLA, viral particle, wildtype, endogenous, VIRUS Schmidt L Tuting C Kyrilis FL Hamdi F Semchonok DA Hause G Meister A Ihling C Stubbs MT Sinz A Kastritis PL Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Commun Biol UK 7 557 557 2024 38730276 doi:10.1038/s42003-024-06204-7 2399-3642 Schmidt L Tuting C Kyrilis FL Hamdi F Semchonok DA Hause G Meister A Ihling C Stubbs MT Sinz A Kastritis PL Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Commun Biol UK 7 557 557 2024 38730276 doi:10.1038/s42003-024-06204-7 2399-3642 Schmidt L Tuting C Kyrilis FL Hamdi F Semchonok DA Hause G Meister A Ihling C Shah PNM Stubbs MT Sinz A Stuart DI Kastritis PL Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts Biorxiv US 2022 doi:10.1101/2022.07.15.498668 2692-8205 8a5t FULLOVERLAP Saccharomyces cerevisiae virus L-A Saccharomyces cerevisiae virus L-A 0 1 Saccharomyces cerevisiae virus L-A Saccharomyces cerevisiae VIRUS-LIKE PARTICLE SPECIES false false Major capsid protein Saccharomyces cerevisiae 0.076070031 2 LEVO MLRFVTKNSQDKSSDLFSICSDRGTFVAHNRVRTDFKFDNLVFNRVYGVSQKFTLVGNPTVCFNEGSSYLEGIAKKYLTL DGGLAIDNVLNELRSTCGIPGNAVASHAYNITSWRWYDNHVALLMNMLRAYHLQVLTEQGQYSAGDIPMYHDGHVKIKLP VTIDDTAGPTQFAWPSDRSTDSYPDWAQFSESFPSIDVPYLDVRPLTVTEVNFVLMMMSKWHRRTNLAIDYEAPQLADKF AYRHALTVQDADEWIEGDRTDDQFRPPSSKVMLSALRKYVNHNRLYNQFYTAAQLLAQIMMKPVPNCAEGYAWLMHDALV NIPKFGSIRGRYPFLLSGDAALIQATALEDWSAIMAKPELVFTYAMQVSVALNTGLYLRRVKKTGFGTTIDDSYEDGAFL QPETFVQAALACCTGQDAPLNGMSDVYVTYPDLLEFDAVTQVPITVIEPAGYNIVDDHLVVVGVPVACSPYMIFPVAAFD TANPYCGNFVIKAANKYLRKGAVYDKLEAWKLAWALRVAGYDTHFKVYGDTHGLTKFYADNGDTWTHIPEFVTDGDVMEV FVTAIERRARHFVELPRLNSPAFFRSVEVSTTIYDTHVQAGAHAVYHASRINLDYVKPVSTGIQVINAGELKNYWGSVRR TQQGLGVVGLTMPAVMPTGEPTAGAAHEELIEQADNVLVE P32503 singleParticle particle 0.3 7.4 200.0 CH3COONH4 Ammoniumacetate
pH of the buffer was adjusted with NaOH buffer was filtered and sonicated
 Quantifoil R2/1 COPPER 200 CARBON HOLEY ARRAY GLOW DISCHARGE AIR 0.04 ETHANE 95 277.15 FEI VITROBOT MARK IV
blot force 2 and blot time 6 s before plunging.
heterogenous cell extract
 TFS GLACIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 1.0 2.0 92000.0 89297.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 118.0 FEI FALCON III (4k x 4k) INTEGRATING 4096 4096 2 7020 3.61 30.0 1 2725140 1M1C 3.78 FSC 0.143 CUT-OFF cryoSPARC v3.3 1020420 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_15189.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 602.0352 602.0352 602.0352 90.0 90.0 90.0 X Y Z -1.0439649 3.451766 0.013144757 0.27169263 1.5678 1.5678 1.5678 1.1 AUTHOR Icosahedral symmetrized map for the viral capsid of the Saccharomyces cerevisiae L-A helper virus 1M1C PDB experimental model RIGID BODY FIT
The initial model was rigid-fitted by ChimeraX and refined by iterative cycles of Coot and PHENIX.
REAL emd_15189_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 602.0352 602.0352 602.0352 90.0 90.0 90.0 X Y Z -0.52907324 1.8119897 0.0015646372 0.23635608 1.5678 1.5678 1.5678 AUTHOR Icosahedral symmetrized map for the viral capsid of the Saccharomyces cerevisiae L-A helper virus - Half Map B emd_15189_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 602.0352 602.0352 602.0352 90.0 90.0 90.0 X Y Z -0.5444305 1.7926624 0.001495722 0.2357421 1.5678 1.5678 1.5678 AUTHOR Icosahedral symmetrized map for the viral capsid of the Saccharomyces cerevisiae L-A helper virus - Half Map A