2024-03-06 REL RCSB RCSB RCSB 2016-05-16 2016-06-08 2016-07-13 2024-03-06 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI011219 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI104317 United States CryoEM structure of the native empty particle of a human rhinovirus C Liu Y Hill MG virus, jelly roll Liu Y Hill MG Klose T Chen Z Watters K Bochkov YA Jiang W Palmenberg AC Rossmann MG Atomic structure of a rhinovirus C, a virus species linked to severe childhood asthma. Proc.Natl.Acad.Sci.USA US 113 8997 9002 2016 27511920 doi:10.1073/pnas.1606595113 1091-6490 0040 PNASA6 EMD-8189 other EM volume 5jzg FULLOVERLAP Rhinovirus C15a Rhinovirus C15a 0 1 2 3
The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa cells expressing the RV-C receptor CDHR3 via multiple passage. The derivative was the RV-C15a virus.
Rhinovirus C15a Homo sapiens 5.8 Capsid (p3) 300.0 3 VIRUS-LIKE PARTICLE STRAIN false true Capsid protein VP1 Rhinovirus C 0.031802622999999995 1 Homo sapiens LEVO NNDDPVENFVESTLKEVLVVPDTKPSGPQHTTKPSILGAMEIGASSNATPESTIETRYVYNTNTNAEADVEMFLGRSALW GKVTLTRQYAKWEINFQEQAHIRKKFEFFTYLRFDMEVTIVTNNKGLMQIMFVPPGIDHPETHDDRKWDSASNPSVFFQP KSGFPRFTIPFTGLASAYYMFYDGYDKPKGSDNNEYGIAPTNDMGLLCFRTLDNSGGNDVKIYVKPKHITAWVPRPPRAT QYTHKYSTNYHYKPNSSGPDEHVLKDRHFIKTRPLISSA E5D8F2 Capsid protein VP3 Rhinovirus C 0.025965037 1 Homo sapiens LEVO GLPTRLPSGSQQFMTTEDEQSPNILPGFHPSKKIHIPGMITNVMHMARVDSFIPINNIQGEVGKVSMYYITVTKKTVTER ILVLPLEMSNTLFATTLLGEVLNYYANWSGSITITFMCVCDAFSTGKFLVAYTPPGGKLPEDRKQAMLGVHIIWDLGLQS SCTIVVPWISSGFYRRTKADSFTHGGYVSLWYQTAFVPPVSGGTGSILATCSACPDMSVRMLRDSPMMEQKNELQ E5D8F2 Capsid protein VP0 Rhinovirus C 0.036247343999999994 1 Homo sapiens LEVO GAQVSRQNNGTHENGVTASNGSVIKYFNINYYKDSASSGLSRQDFSQDPSKFTQPLVDTLTNPALMSPSVEACGYSDRLK QITIGNSTITTQDSLHTVLAYGEWPTYLSDIDATSVDKPTHPETSADRFYTLDSVEWQVGSHGWWWKLPDALKDMGVFGQ NMYYHSMGRSGFIIHTQCNATKFHSGALIVAVIPEHQLAYVGGVKVNVGYDHTHPGQSGHQIRGPSQSNDRSGGKPDEDP LFNCNGTLLGNITIFPHQIINLRTNNSSTIVVPYINCVPMDNMLKHNNLSLVIIPLVPLRPGSSGINSVPITVTIAPYKS EFSGAMEAQRQ E5D8F2 singleParticle particle 1 8.0 20.0 C4H11NO3 Tris 120.0 NaCl sodium chloride 1.0 C10H16N2O8 EDTA Ultra thin Lacey carbon COPPER 400 CARBON LACEY CARBON CONTINUOUS GLOW DISCHARGE AIR 0.02 ETHANE 80 298 GATAN CRYOPLUNGE 3 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.7000000000000001 3.5 14000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3-70 3 3614 14.0 25.7 1 24882
A mixed population of empty particles, full particles, and junk
For each of the half subsets, random orientation was assigned to each of the 150 randomly selected particles. The resulting models were much like a ball in appearance. Refinement was then performed by searching for the best orientation and particle center of each particle image relative to the current 3D reconstructions using projection matching. Three of these structures were selected for further refinement using all the available particle images in the half subset. These structures converged to roughly the same reconstruction. One of these structures was randomly chosen to extend the refinement.
 I 3.16 FSC 0.143 CUT-OFF jspr 3614 PROJECTION MATCHING 6.5 jspr PROJECTION MATCHING 0.5 jspr 156 RELION 1.3 emd_8184.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 499.19998 499.19998 499.19998 90.0 90.0 90.0 X Y Z -48.974299999999999 67.214264 0.06435112 3.4875524 1.04 1.04 1.04 13.4 AUTHOR CryoEM structure of the native empty particle of a human rhinovirus C RIGID BODY FIT Correlation coefficient REAL