Cryo-electron tomography and subtomogram averaging of Rous-Sarcoma- Virus deltaMBD virus-like particles
ELECTRON MICROSCOPY
Sample
IMMATURE ROUS-SARCOMA VIRUS GAG PARTICLES
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK II
Cryogen Name
ETHANE
Sample Vitrification Details
DEGASSED C-FLAT 2 2-3C GRIDS WERE GLOW DISCHARGED FOR 30 SECONDS AT 20 MA. VIRUS SOLUTION WAS DILUTED IN OBS CONTAINING 10NM COLLOIDAL GOLD. 2.5UL OF ...
DEGASSED C-FLAT 2 2-3C GRIDS WERE GLOW DISCHARGED FOR 30 SECONDS AT 20 MA. VIRUS SOLUTION WAS DILUTED IN OBS CONTAINING 10NM COLLOIDAL GOLD. 2.5UL OF THIS MIXTURE WAS APPLIED TO A GRID. BLOTTING TIME 2.5 SECONDS.
3D Reconstruction
Reconstruction Method
TOMOGRAPHY
Number of Particles
8375
Reported Resolution (Å)
7.7
Resolution Method
Other Details
RECONSTRUCTION CARRIED OUT USING SUBTOMOGRAM AVERAGING. SUBTOMOGRAM AVERAGING WAS PERFORMED USING SCRIPTS DERIVED FROM THE AV3 (FOERSTER, ET AL) TOM ( ...
RECONSTRUCTION CARRIED OUT USING SUBTOMOGRAM AVERAGING. SUBTOMOGRAM AVERAGING WAS PERFORMED USING SCRIPTS DERIVED FROM THE AV3 (FOERSTER, ET AL) TOM (NICKELL, ET AL) AND DYNAMO (CASTANO-DIEZ, ET AL) PACKAGES. STRUCTURES FOR P10 AND CA-NTD (PDB 1P7N) AND CA-CTD (PDB 3G1I, ONE MONOMER) WERE RIGID BODY DOCKED INTO THE EM-MAP USING THE FIT-IN-MAP OPTION IN CHIMERA. REDUNDANT RESIDUES OF THE ANTIPARALLEL DIMER OF PDB 1P7N WERE REMOVED. MISSING RESIDUES IN THE HELIX 7-HELIX 8 LINKER REGION OF CA, THE CONNECTION LOOP BETWEEN P10 AND CA-NTD AND RESIDUES UPSTREAM OF THE HELIX IN P10 WERE MANUALLY MODELED USING COOT. THE FIT WAS FURTHER REFINED USING MOLECULAR DYNAMICS FLEXIBLE FITTING. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3101. (DEPOSITION ID: 13603).
