REL PDBe PDBe PDBe 2013-08-13 2013-09-11 2013-10-02 2013-10-16 Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery Peralta B Gil-Carton D Castano-Diez D Bertin A Boulogne C Oksanen HM Bamford DH Abrescia NGA virus; structural virology; viral genome delivery; proteo-lipidic structures; membrane remodelling; nanotube formation; single-particle tomography; cellular tomography Peralta B Gil-Carton D Castano-Diez D Bertin A Boulogne C Oksanen HM Bamford DH Abrescia NGA Mechanism of membranous tunnelling nanotube formation in viral genome delivery. PLOS BIOL. 11 e1001667 e1001667 2013 24086111 doi:10.1371/journal.pbio.1001667 Abrescia NG Cockburn JJ Grimes JM Sutton GC Diprose JM Butcher SJ Fuller SD SanMartin C Burnett RM Stuart DI Bamford DH Bamford JK Insights into assembly from structural analysis of bacteriophage PRD1 NATURE 432 68 74 2004 15525981 doi:10.1038/nature03056 Cockburn JJ Abrescia NG Grimes JM Sutton GC Diprose JM Benevides JM Thomas GJ Bamford JK Bamford DH Stuart DI Membrane structure and interactions with protein and DNA in bacteriophage PRD1. NATURE 432 122 125 2004 15525993 doi:10.1038/nature03053 Lipid-containing bacteriophage PRD1 Lipid-containing bacteriophage PRD1
Please keep in mind that these are PRD1 particles with a protruding tube. Therefore the icosahedral symmetry is broken and never applied during data processing and averaging
A pseudo T=25 assembly 1 70 Enterobacteria phage PRD1
Infects both Escherichia coli and Salmonella enterica
Enterobacteria phage PRD1 Escherichia coli BACTERIA(EUBACTERIA) 70 P3 VIRION SPECIES false false bacteriophage PRD1 subtomogramAveraging particle 0.6 7.2
20 mM Phosphate Buffer 1 mM MgCl2
200 mesh QUANTIFOIL R 2/1 (or R 3.5/1) copper grid, glow discharged in air atmosphere
 ETHANE 95 120 FEI VITROBOT MARK III Blot for 4 seconds before plunging JEOL 2200FS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2 5.0 8.0 25000.0 34138.0 GATAN LIQUID NITROGEN 80 105 99 Objective lens astigmatism was corrected at 120,000 times magnification In-column Omega filter 10.0 30.0 2012-01-04 GATAN ULTRASCAN 4000 (4k x 4k) OTHER 100 16. -64 64
The tube was use as pivot for initial alignment. Please see details in primary reference.
C1 OTHER 64.0 FSC 0.5 CUT-OFF IMOD, Dynamo 174 emd_2438.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 96 96 96 0 0 0 96 96 96 844.80005 844.80005 844.80005 90.0 90.0 90.0 X Y Z -2.83609939 3.94621778 -0.19220899 0.84541529 8.8 8.8 8.8 1.5 AUTHOR Contour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. The recommended contour level for the visualization of the internal vesicle is about 0.35 sigma
::::EMDATABANK.org::::EMD-2438::::
 1W8X RIGID BODY FIT Chimera
For the docking, please, see the protocol described in the primary reference
REAL