REL PDBe PDBe PDBe 2015-10-14 2015-12-23 2015-12-23 2015-12-23 Sub-tomogram averaging of electron cryo-microscopic data taken from focused-ion beam milled lamellae of nuclei of Pseudorabies virus (PrV) nuclear egress complex-expressing cells Hagen C Siebert CA Dent KC Vasishtan D Zeev Ben Mordehai T Grange M Klupp BG Mettenleiter T Gruenewald K alphaherpesvirinae; herpesvirus simplex; HSV-1; pseudorabies virus; PrV; nuclear egress complex; nuclear envelope; nucleoplasmic reticulum; inner nuclear membrane; UL31; UL34; vesicle transport; nucleo-cytoplasmic transport; nanovesicles; cryoEM; cryoET; electron cryo-microscopy; electron cryo-tomography; cryoFIB; focused ion beam milling; FIB-SEM Hagen C Dent KC Zeev Ben Mordehai T Grange M Bosse JB Whittle C Klupp BG Siebert CA Vasishtan D Baeuerlein FJB Cheleski J Werner S Guttmann P Rehbein S Henzler K Demmerle J Adler B Koszinowski U Schermelleh L Schneider G Enquist LW Plitzko JM Mettenleiter TC Gruenewald K Structural Basis of Vesicle Formation at the Inner Nuclear Membrane Cell Reports 2015 doi:10.1016/j.cell.2015.11.029 Zeev-Ben-Mordehai T Weberruss M Lorenz M Cheleski J Hellberg T Whittle C El Omari K Vasishtan D Dent KC Harlos K Franzke K Hagen C Klupp B Antonin W Mettenleiter TC Gruenewald K Crystal structure of the herpesvirus nuclear egress complex provides insights into inner nuclear membrane remodelling Cell Reports 2015 doi:10.1016/j.celrep.201 5.11.008 vesicles coated with pUL31/pUL34 heterodimers vesicles coated with pUL31/pUL34 heterodimers
porcine epithelial-like embryonic EFN-R kidney cells stably co-expressing PrV UL31 and UL34, the latter fused with GFP (cell line designated as BK/EF/UL31/34gfp catalogue No. RIE 1083 of the Collection of Cell Lines in Veterinary Medicine at the FLI, Greifswald-Insel Riems, Germany)
coat of ~500 hexamers of pUL31/pUL34 heterodimers per vesicle 2 Nuclear envelope
two proteins (pUL31 and pUL34) of pseudorabies virus (PrV) are co-expressed in the cells forming there the herpesviral nuclear egress complex lining as a coat perinuclear vesicles
heterodimer IPR021152 IPR007626 false Sus scrofa Pig Kidney Epithelial-like embryonic Nucleus Nuclear membranes 0.060 0.060 Suid herpesvirus 1
two proteins (pUL31 and pUL34) of pseudorabies virus (PrV) are co-expressed in the cells forming there the herpesviral nuclear egress complex lining as a coat perinuclear vesicles
Suid herpesvirus 1 Sus scrofa VERTEBRATES VIRION OTHER true false Aujeszky's disease virus subtomogramAveraging cell NEGATIVE
no staining
glow discharged standard 3.05 mm electron microscopy 200 mesh gold grids covered with a perforated carbon foil (R2/1; Quantifoil Micro Tools GmbH, Jena, Germany); focused-ion beam milled lamella
 ETHANE-PROPANE MIXTURE HOMEMADE PLUNGER two days of incubation (37 degree C, 5 % CO2) in plastic microscope slide growth chambers (mue-slide 2x9 well; Ibidi GmbH) before cryo-immobilization blotted manually with a bent strip of Whatman No. 1 filter paper from the non-coated grid side for 2 to 3 s immediately before vitrification by the gravity-driven plunging apparatus in a ethane/propane mixture cooled by liquid nitrogen FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2 -6.0 -6.0 22500.0 52650.0 OTHER Gatan GIF 2 0.0 20.0
2048 x 2048
2013-04-26 GATAN MULTISCAN 35 114
electron cryo-tomographic tilt series with 3 degree spacing
32. -50 52
'Particle' positions and orientations were initially approximated by modelling intraluminal vesicles as a set of points distributed over a sphere. After orienting particles to align their primary axes (defined as normal to the vesicle membrane) to the Y-axis, iterative 3D orientation search and translational alignment was carried out using PEET according to standard methods. Particles from each vesicle were aligned and average independently. For further information please refer to the primary citation.
C6 OTHER 35.0 OTHER IMOD 300 emd_3197.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 20 20 20 -2 0 0 20 20 20 228.0 228.0 228.0 90.0 90.0 90.0 X Y Z -4.13374567 5.57673693 0.78361201 2.39995289 11.4 11.4 11.4 1.9 AUTHOR Sub-tomogram average of nuclear egress complex from vesicles observed inside nuclei of cells co-expressing PrV UL31 and UL34 by focus-ion beam milling and electron cryo-tomography.
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 5E8C A B RIGID BODY FIT TEMPy, Chimera
A single heterodimer was fitted in 144000 different positions, and symmetrized into a hexameric lattice. Each was scored by the number of atomic clashes with neighbouring heterodimers and the amount of protrusion from the map. The highest ranking fit was chosen as the final fit.
Minimisation of atomic clashes and protrusion from map REAL
emd_3197.png