2024-05-22 REL PDBe PDBe PDBe 2020-01-08 2020-02-26 2020-02-26 2024-05-22 Wellcome Trust 202231/Z/16/Z United Kingdom Cryo-EM structure of Pf4 bacteriophage coat protein with single-stranded DNA Tarafder AK von Kugelgen A Bacteriophage, helical, filamentous, VIRUS Tarafder AK von Kugelgen A Mellul AJ Schulze U Aarts DGAL Bharat TAM Phage liquid crystalline droplets form occlusive sheaths that encapsulate and protect infectious rod-shaped bacteria. Proc.Natl.Acad.Sci.USA US 117 4724 4731 2020 32071243 doi:10.1073/pnas.1917726117 1091-6490 0040 PNASA6 6tup FULLOVERLAP Pseudomonas virus Pf1 Pseudomonas virus Pf1 0 1 2 Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) Coat protein B (CoaB) 62.0 VIRION STRAIN false false Pseudomonas virus Pf1 1 1 Pseudomonas virus Pf1 DNA 1 2 Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) Coat protein B of bacteriophage Pf1 Pseudomonas virus Pf1 0.004612393 1 LEVO GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA Q9I5K5 DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3') Pseudomonas aeruginosa PAO1 0.001834283
Model of pf4 single-stranded DNA genome
1 (DA)(DA)(DA)(DA)(DA)(DA) DNA helical filament 5 7.4 8.0 NaCl sodium chloride 0.2 KCl potassium chloride 1.15 Na2HPO4 sodium phosphate dibasic 0.2 KH2PO4 potassium phosphate monobasic
1x Phosphate buffered saline
 Quantifoil R2/2 COPPER/RHODIUM 200 CARBON HOLEY GLOW DISCHARGE AIR 0.03
20 second glow discharge at 15 mA in a LeicaEM ACE200
 ETHANE 100 283 FEI VITROBOT MARK IV
Samples for cryo-EM were prepared by pipetting 2.5 ul of the sample onto freshly glow-discharged Quantifoil grids (Cu/Rh R2/2, 200 mesh). Grids were blotted for 2.5 seconds with a blot force of -15, 0.5 second drain and 0 second wait times..
Filamentous phage purified from source
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 -1.0 -1.0 -3.0 -3.0 105000.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 80.0 GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 1-40 2 4110 10.0 43.0 1 1 3.14 65.9 C1 FOURIER SPACE 3.2 FSC 0.143 CUT-OFF RELION 3.0 185002 351381 RELION 2.0
Fourier-Bessel indexing
 NOT APPLICABLE RELION 2.0 emd_10593.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 552.0 552.0 552.0 90.0 90.0 90.0 X Y Z -0.03785945 0.10565073 -0.0000120200175 0.0022136576 1.38 1.38 1.38 0.025 AUTHOR BACKBONE TRACE
The helical filament symmetry is only applied to the Pf4 coat protein and not the DNA. The reason for this is that the DNA bases are not resolved clearly due to averaging along the ssDNA genome of the phage, meaning that refinement of the protein into the map is of a higher quality than the ssDNA, where a poly-adenine model has been built.
Correlation coefficient REAL 93.739999999999995