2024-01-31 REL PDBe PDBe PDBe 2023-04-07 2024-01-24 2024-01-24 2024-01-31 Slovenian Research Agency P1-0391 Slovenia Slovenian Research Agency J7-7248 Slovenia Ministry of Education, Youth and Sports of the Czech Republic LM2018127 Czech Republic Global refinement of cubic assembly from truncated PVY coat protein with K176C mutation Kavcic L Kezar A Podobnik M cubes, trCP, K176C, Potyvirus, PVY, VIRUS LIKE PARTICLE Kavcic L Kezar A Koritnik N Znidaric MT Klobucar T Vicic Z Merzel F Holden E Benesch JLP Podobnik M From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Commun Chem UK 7 14 14 2024 38233506 doi:10.1038/s42004-024-01100-x 2399-3669 EMD-17063 other EM volume
EMD-17063 contains locally refined map and model of one cubic face
 8opj FULLOVERLAP truncated coat protein (dN49C40) with C-terminal His tag and K176C mutation truncated coat protein (dN49C40) with C-terminal His tag and K176C mutation 0 1
structurally homogenous cubic particles
Potato virus Y strain NTN 1.315 Genome polyprotein (Fragment) Potato virus Y strain NTN NTN 0.022360423999999997 48 Escherichia coli BL21(DE3) LEVO GITSKMRMPKSKGATVLNLEHLLEYAPQQIDISNTRATQSQFDTWYEAVQLAYDIGETEMPTVMNGLMVWCIENGTSPNI NGVWVMMDGDEQVEYPLKPIVENAKPTLRQIMAHFSDVAEAYIEMRNCKEPYMPRYGLVRNLRDGSLARYAFDFYEVTSR TPVRAREAHIQMKAAALKSENLYFQGLEHHHHHH A0A0A7DIW7 singleParticle particle 4 7.4
1.8 mM KH2PO4, 10.1 mM Na2HPO4, 140 mM NaCl, 2.7 mM KCl, pH 7.4
 Quantifoil R2/2 COPPER 200 ETHANE TFS KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 0.3 3.6 165000.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 9480 4.0 32.0 1 1580128
Initial model was obtained by ab-initio reconstruction
 O 2.99 FSC 0.143 CUT-OFF cryoSPARC 210779 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD emd_17062.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 493.2 493.2 493.2 90.0 90.0 90.0 X Y Z -0.030798942 1.9615546 0.0011881099 0.024587259 0.822 0.822 0.822 0.1 AUTHOR final trCPK176C cubic particle global refinement cryoEM map after DeepEMhancer post-processing (O) emd_17062_msk_1.map emd_17062_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 493.2 493.2 493.2 90.0 90.0 90.0 X Y Z -0.1375136 0.6027834 -0.0010152449 0.024388554 0.822 0.822 0.822 AUTHOR trCPK176C cubic particle raw cryoEM map (O) emd_17062_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 493.2 493.2 493.2 90.0 90.0 90.0 X Y Z -0.9565223 1.8778878 -0.0010152448 0.049099445 0.822 0.822 0.822 AUTHOR trCPK176C cubic particle global refinement sharp cryoEM map (O) emd_17062_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 493.2 493.2 493.2 90.0 90.0 90.0 X Y Z -0.4683573 0.6736679 0.0008314806 0.048259564 0.822 0.822 0.822 AUTHOR trCPK176C cubic particle half B cryoEM map emd_17062_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 493.2 493.2 493.2 90.0 90.0 90.0 X Y Z -0.40795353 0.76953036 0.0008261174 0.048287492 0.822 0.822 0.822 AUTHOR trCPK176C cubic particle half A cryoEM map