REL PDBe PDBe PDBe 2015-07-20 2015-08-05 2015-08-12 2015-10-07 Cryo-electron tomography and subtomogram averaging of Rous-Sarcoma-Virus deltaMBD virus-like particles Schur FKM Dick RA Hagen WJH Vogt VM Briggs JAG Retrovirus, Rous-Sarcoma virus, immature retrovirus, virus-like-particle, capsid Schur FKM Dick RA Hagen WJH Vogt VM Briggs JAG The Structure of Immature Virus-Like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the p10 Domain in Assembly J.VIROL. 89 10294 10302 2015 26223638 doi:10.1128/JVI.01502-15 5a9e FULLOVERLAP Immature-like Rous-Sarcoma Virus Gag particles Immature-like Rous-Sarcoma Virus Gag particles Homohexameric 1 Rous-Sarcoma Virus deltaMBD Gag protein Rous sarcoma virus RSV 0.052 Hexamer true Escherichia coli BL21 P03322 subtomogramAveraging particle 5 6.5
MES pH6.5, 100mM NaCl,2uM ZnCl2 2mM TCEP
C-Flat 2/2-#c grids, glow discharged for 30 sec in 20mA
 ETHANE 100 FEI VITROBOT MARK II Degassed C-Flat 2/2-3C grids were glow discharged for 30 seconds at 20 mA. Virus solution was diluted in PBS containing 10nm colloidal gold. 2.5 ul of this mixture was applied to a grid. Blotting time: 2 seconds FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.5 5.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER GATAN GIF 2002 0.0 20.0 2014-09-10 GATAN MULTISCAN 34
Tilt series consisted of 21 or 31 micrographs.
 -45 45
Reconstruction carried out using subtomogram averaging. Subtomogram averaging was performed using scripts from the TOM (Nickell et al, 2005), AV3 (Foerster et al, 2005) and Dynamo (Castano-Diez, 2012) packages. Subtomograms were extracted from the surface of the virus-like parcticles with the radius corresponding to the radius of the particles.
C6 OTHER 7.7 OTHER IMOD, AV3, TOM, Dynamo
Reconstruction carried out using subtomogram averaging. Subtomogram averaging was performed using scripts from the TOM (Nickell et al, 2005), AV3 (Foerster et al, 2005) and Dynamo (Castano-Diez, 2012) packages. Subtomograms were extracted from the surface of the virus-like parcticles with the radius corresponding to the radius of the particles.
8375
Phase flipping of individual tilts
 1 emd_3101.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 120 120 120 0 0 0 120 120 120 248.4 248.4 248.4 90.0 90.0 90.0 X Y Z -6.57726717 8.24688911 -0.00028003 0.7611295 2.07 2.07 2.07 2.0 AUTHOR Subtomogram averaging reconstruction of immature RSV capsid from virus-like particles
::::EMDATABANK.org::::EMD-3101::::
 1p7n FLEXIBLE FIT Chimera, VMD, MDFF
Structures for p10 and CA-NTD (PDB 1P7N) and CA-CTD (PDB 3G1I, one monomer) were rigid body docked into the EM-density using the "Fit in map" option in chimera. Redundant residues of the antiparallel dimer of PDB 1P7N were removed. Missing residues in the helix7/helix8 linker region of CA, the connection loop between p10 and CA-NTD and residues upstream of the helix in p10 were manually modelled in Coot. The fit was further refined using Molecular Dynamics Flexible Fitting.
REAL 3G1I FLEXIBLE FIT Chimera, VMD, MDFF
Structures for p10 and CA-NTD (PDB 1P7N) and CA-CTD (PDB 3G1I, one monomer) were rigid body docked into the EM-density using the "Fit in map" option in chimera. Redundant residues of the antiparallel dimer of PDB 1P7N were removed. Missing residues in the helix7/helix8 linker region of CA, the connection loop between p10 and CA-NTD and residues upstream of the helix in p10 were manually modelled in Coot. The fit was further refined using Molecular Dynamics Flexible Fitting.
REAL
emd_3101.tif