2026-08-19 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.page_first _em_admin.last_update RCSB RCSB 2025-04-15 2026-07-08 2026-07-08 2026-08-19 Sao Paulo Research Foundation (FAPESP) 2017/15340-2 Brazil Sao Paulo Research Foundation (FAPESP) 2022/08730-7 Brazil Sao Paulo Research Foundation (FAPESP) 2017/17303-7, 2021/10577-0 Brazil Sao Paulo Research Foundation (FAPESP) 2023/13894-1, 2023/16089-2 Brazil Cryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Bacteriophage-Associated Proteins with Shell-Like Assemblies Guzzo CR Araujo GG Merighi DGS D18 symmetry, shell-like structure, DUF2303, YfdQ, VIRAL PROTEIN Merighi DGS Pompeu GC Araujo GG Silva de Souza A Sgro GG Farah CS Guzzo CR Cryo-EM structure of YfdQ reveals a widespread family of bacteriophage-associated proteins with shell-like assemblies. Structure UK 34 1159 2026 42309054 doi:10.1016/j.str.2026.05.009 0969-2126 2005 STRUE6 9o7m FULLOVERLAP EMDB EMD-70204 associated EM volume
Cryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Bacteriophage-Associated Proteins with Shell-Like Assemblies
 YfdQ pprotein complex YfdQ pprotein complex 0 1
YfdQ
Caudoviricetes phiXacm4-11 1.059 YfdQ Protein Caudoviricetes phiXacm4-11 0.029457115 36 LEVO MDKSAIEAIQDSSAAAAKATQEQIPAGITHLVAVPNGVTLQNVEISLAGRTRFRGKLVTSSIPDFVTYVKNREGGHGFID TDKLGATVFFNLGDADKPGHADHTARLTLQATPAYLAMLAAGGKAFSQRDALDFIEDWSHLIGAHQVSDDGAFSPIPLAR AIAAIRKVKIKAESTTEQTEGNFQQSRSVLESVAASSDEGLPDVLSFRTEPYLGLPERTFHMRVSVSTTGREPSLRFRVI ALEQEQDEIAKQFKALLLGEVGEAASMTIGTFTP singleParticle particle 7.5
50 mM Tris-HCl, 100 mM NaCl, 10 mM MgSO47(H2O), pH 7.5
 ETHANE 100 295
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..
native particles produced during phiXacm4-11 infection
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 0.001 0.5 2.0 FEI FALCON III (4k x 4k) COUNTING 44.89
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.
 1
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.
cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION
AlphaFold 3
 D18 3.9 FSC 0.143 CUT-OFF 237960 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_70204.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 395.6 395.6 395.6 90.0 90.0 90.0 X Y Z -0.15722173 0.8198009 0.002862633 0.063914165 0.86 0.86 0.86 0.422 AUTHOR Raw map RIGID BODY FIT REAL emd_70204_msk_1.map emd_70204_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 395.6 395.6 395.6 90.0 90.0 90.0 X Y Z -0.32403442 0.8707594 0.0035254841 0.06601386 0.86 0.86 0.86 AUTHOR Half map emd_70204_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 395.6 395.6 395.6 90.0 90.0 90.0 X Y Z -0.24647316 0.8699961 0.003516642 0.06613085 0.86 0.86 0.86 AUTHOR Half map