2024-05-15 REL PDBe PDBe PDBe 2017-01-14 2017-01-25 2017-03-22 2024-05-15 dsRNA bacteriophage phi6 nucleocapsid Sun Z El Omari K icosahedral virus capsid shell, virus Sun Z El Omari K Sun X Ilca SL Kotecha A Stuart DI Poranen MM Huiskonen JT Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Nat Commun UK 8 14814 14814 2017 28287099 doi:10.1038/ncomms14814 2041-1723 5muu FULLOVERLAP Pseudomonas phage phi6 Pseudomonas phage phi6 0 1 2 3
The viral envelope was removed by Triton X-114 extraction
Pseudomonas phage phi6 Pseudomonas syringae pv.phaseolicola HB10Y Outer shell 565.0 13 Inner shell 500.0 1 VIRION SPECIES true false Major inner protein P1 Pseudomonas phage phi6 0.08508071099999999 2 LEVO MFNLKVKDLNGSARGLTQAFAIGELKNQLSVGALQLPLQFTRTFSASMTSELLWEVGKGNIDPVMYARLFFQYAQAGGAL SVDELVNQFTEYHQSTACNPEIWRKLTAYITGSSNRAIKADAVGKVPPTAILEQLRTLAPSEHELFHHITTDFVCHVLSP LGFILPDAAYVYRVGRTATYPNFYALVDCVRASDLRRMLTALSSVDSKMLQATFKAKGALAPALISQHLANAATTAFERS RGNFDANAVVSSVLTILGRLWSPSTPKELDPSARLRNTNGIDQLRSNLALFIAYQDMVKQRGRAEVIFSDEELSSTIIPW FIEAMSEVSPFKLRPINETTSYIGQTSAIDHMGQPSHVVVYEDWQFAKEITAFTPVKLANNSNQRFLDVEPGISDRMSAT LAPIGNTFAVSAFVKNRTAVYEAVSQRGTVNSNGAEMTLGFPSVVERDYALDRDPMVAIAALRTGIVDESLEARASNDLK RSMFNYYAAVMHYAVAHNPEVVVSEHQGVAAEQGSLYLVWNVRTELRIPVGYNAIEGGSIRTPEPLEAIAYNKPIQPSEV LQAKVLDLANHTTSIHIWPWHEASTEFAYEDAYSVTIRNKRYTAEVKEFELLGLGQRRERVRILKPTVAHAIIQMWYSWF VEDDRTLAAARRTSRDDAEKLAIDGRRMQNAVTLLRKIEMIGTTGIGASAVHLAQSRIVDQMAGRGLIDDSSDLHVGINR HRIRIWAGLAVLQMMGLLSRSEAEALTKVLGDSNALGMVVATTDIDPSL P11126 Packaging enzyme P4 Pseudomonas phage phi6 0.035198426 1 LEVO MPIVVTQAHIDRVGIAADLLDASPVSLQVLGRPTAINTVVIKTYIAAVMELASKQGGSLAGVDIRPSVLLKDTAIFTKPK AKSADVESDVDVLDTGIYSVPGLARKPVTHRWPSEGIYSGVTALMGATGSGKSITLNEKLRPDVLIRWGEVAEAYDELDT AVHISTLDEMLIVCIGLGALGFNVAVDSVRPLLFRLKGAASAGGIVAVFYSLLTDISNLFTQYDCSVVMVVNPMVDAEKI EYVFGQVMASTVGAILCADGNVSRTMFRTNKGRIFNGAAPLAADTHMPSMDRPTSMKALDHTSIASVAPLERGSVDTDDR NSAPRRGANFSL P11125 3.6.1.15 Major outer capsid protein Pseudomonas phage phi6 0.016018418 10 LEVO MLLPVVARAAVPAIESAIAATPGLVSRIAAAIGSKVSPSAILAAVKSNPVVAGLTLAQIGSTGYDAYQQLLENHPEVAEM LKDLSFKADEIQPDFIGNLGQYREELELVEDAARFVGGMSNLIRLRQALELDIKYYGLKMQLNDMGYRS P07579 singleParticle particle 3 7.2 C-flat COPPER CARBON HOLEY ARRAY GLOW DISCHARGE AIR ETHANE FEI VITROBOT MARK III FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.0 0.3 3.0 160000.0 37037.0 OTHER NITROGEN 80.0 120.0 GIF Quantum LS 0 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3710 1-22 900 0.2 0.73 1 16466 EMD-1207 I FOURIER SPACE 4.0 FSC 0.143 CUT-OFF RELION 1.3 13291 PROJECTION MATCHING RELION 1.3 PROJECTION MATCHING RELION 1.3 4 RELION 1.3 emd_3571.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 691.2 691.2 691.2 90.0 90.0 90.0 X Y Z -0.07375267 0.14329888 0.00020935167 0.008287506 1.35 1.35 1.35 0.02 AUTHOR dsRNA bacteriophage phi6 nucleocapsid 4K7H A 1-760 PDB experimental model RIGID BODY FIT
The structure of P1 was fitted in the map using COOT as a rigid body in two different positions corresponding to subunits P1A and P1B. P1A and P1B main-chains and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.
REAL AB INITIO MODEL
The structure of P8 (L3 to Y147) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.
REAL AB INITIO MODEL
The structure of P4 C-terminus (R292 to L332) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.