REL RCSB RCSB RCSB 2012-11-30 2012-12-12 2013-04-03 2013-04-03 6.3 A Cryo-EM Structure of a Novel Calicivirus, Tulane Virus Yu G Zhang D Guo F Tan M Jiang X Jiang W Tulane virus, calicivirus, conformational flexibility, single particle cryo-EM, 3-D reconstruction Yu G Zhang D Guo F Tan M Jiang X Jiang W Cryo-EM structure of a novel calicivirus, Tulane virus. PLOS ONE 8 e59817 e59817 2013 23533651 doi:10.1371/journal.pone.0059817 Tulane virus Tulane virus One Tulane virus has 90 dimers forming its icosahedral capsid (T=3). 1 10.4 Tulane virus Tulane virus Macaca mulatta VERTEBRATES 10.4 VP1 400 3 VIRION SPECIES false false singleParticle particle 7.4
137mM NaCl, 2.7mM KCl, 10mM Na2HPO4, 2mM KH2PO4, pH 7.4
 NEGATIVE
Grids with sample floated on 2% uranyl acetate for 30 seconds.
400 mesh copper grid with one lacy carbon layer and one layer of ultra thin carbon on top.
 ETHANE 85 HOMEMADE PLUNGER FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.347 4.891 37000.0 36475.0 FEI TITAN KRIOS AUTOGRID HOLDER 80 85 80 Objective lens astigmatism was corrected at 250,000 magnification using quadrupole stigmator. 0 2011-07-29 KODAK SO-163 FILM NIKON SUPER COOLSCAN 9000 6.35 190 25 16. Liquid nitrogen cooled
4702 Tulane virus particles were selected using combined automated selection with ethan program and manual screening with boxer program in EMAN. The microscope contrast transfer function parameters for each micrograph were first determined using an automated fitting method and then manually verified/corrected using EMAN ctfit graphic program. The entire TV dataset was divided into two halves and processed independently for all the subsequent steps including construction of initial model, 2-D alignment and 3-D reconstruction. De novo initial models were constructed using the random model method in which random particle orientations were assigned and subsequently refined iteratively until convergence. The iterative refinement process including particle alignment and 3-D icosahedral reconstruction was performed using an in-house developed program jspr.py utilizing the EMAN/EMAN2 programs and library functions. The resolution was determined based on the 0.143 cutoff criterion for two truly independent reconstructions.
each particle
 OTHER 6.3 OTHER jspr.py, EMAN, EMAN2 4338 emd_5529.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 612.48 612.48 612.48 90.0 90.0 90.0 X Y Z -14.32884121 20.855964660000001 0.08813742 1.26044631 1.74 1.74 1.74 4.0 AUTHOR Reconstruction of TV virion
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 1IHM A B C RIGID BODY FIT Chimera
Protocol: rigid body. The three chains from 1IHM were first fitted into TV density as a whole rigid body and then divided into dimers, specific chains, domains, and subdomains and fitted.
Correlation REAL
emd_5529.tif