Cryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Bacteriophage-Associated Proteins with Shell-Like Assemblies
Cryo-EM structure of YfdQ reveals a widespread family of bacteriophage-associated proteins with shell-like assemblies.
50 mM Tris-HCl, 100 mM NaCl, 10 mM MgSO47(H2O), pH 7.5
Using CryoSPARC, patch motion correction and patch CTF estimation jobs were run before using a combination of Blob Picker and Template Picker in micrograph subsets to obtain a stack of 369,017 particles after extraction in 460-460 pixel boxes. Rounds of 2D classification were used to select the particles that contributed to the best resolved classes. The chosen 249,600 particles were used to reconstruct an ab Initio model using D18 symmetry inferred from the 2D classes (C1 did not produce shell-like models). Homogeneous refinement using this volume as input and maintaining the symmetry yielded an interpretable model at 3.85 A resolution. To assess possible heterogeneities, a 3D classification job was run (C1 symmetry, 10 classes), but no other shell configurations could be observed. A non-uniform refinement with applied D18 symmetry of the 237,960 particles from the largest class yielded the final 3.44 A resolution map.
Data were acquired using a Titan Krios G3i cryo-electron microscope, 300 kV (Thermo Fisher Scientific), at the LNNano facility, CNPEM, Campinas, Brazil. The microscope was equipped with a 4k-4k CMOS camera, phase plate, spherical aberration corrector, and Falcon 3 detector without energy filter or a K3 detector with energy filter. For the native YfdQ dataset, data collection utilized the Falcon 3 detector in counting mode.
native particles produced during phiXacm4-11 infection
A purified YfdQ proteins were pipetted over Glow-Discharged Quantifoil CU-R2/2 400 Mesh grids with a 2 nm ultrathin carbon layer and vitrified by plunge-freezing using a Vitrobot (Thermo Fisher Scientific). The sample was drained by 3.5 s blot and 0 force, and 4.5 s and 0 force programs.
MDKSAIEAIQDSSAAAAKATQEQIPAGITHLVAVPNGVTLQNVEISLAGRTRFRGKLVTSSIPDFVTYVKNREGGHGFID TDKLGATVFFNLGDADKPGHADHTARLTLQATPAYLAMLAAGGKAFSQRDALDFIEDWSHLIGAHQVSDDGAFSPIPLAR AIAAIRKVKIKAESTTEQTEGNFQQSRSVLESVAASSDEGLPDVLSFRTEPYLGLPERTFHMRVSVSTTGREPSLRFRVI ALEQEQDEIAKQFKALLLGEVGEAASMTIGTFTP
REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
D18 symmetry, shell-like structure, DUF2303, YfdQ, VIRAL PROTEIN