EMD-2379 Experiments and Validation

Structure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction

Subtomogram averaging
Overview of EMD-2379
Sample name: HSV-1 glycoprotein B ectodomain lacking the membrane-proximal region bound to a lipid bilayer
Organism: Human herpesvirus 1
Related EM entry by publication: EMD-2380

Map parameters

Recommended contour level: 2.00 (author)
Number of grid points: 100 × 100 × 100
Voxel size: 4.60 × 4.60 × 4.60 Å
Minimum density: -10.94
Maximum density: 15.956
Average density: 0.00
Standard deviation: 1.00

Sample information

Sample name: HSV-1 glycoprotein B ectodomain lacking the membrane-proximal region bound to a lipid bilayer
Protein: Envelope glycoprotein B

Validation information

Experimental information

 

Image processing

Applied symmetry: C3
Software: Jsubtomo
Number of subtomograms averaged: 996
Reconstruction protocol: Subtomogram averaging
CTF correction: Low pass filter to the first zero crossing of the CTF
Details: The best 730 spikes (of 996) were selected based on constrained cross correlation coefficient and by excluding overlaps. The long axis of the gB spike was assumed to be perpendicular to the plane of the membrane in the refinement. The sub-tomograms were picked manually from tomographic reconstructions of 38 liposomes

Imaging

Session
Microscope model: FEI TECNAI F20
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 100.0
Nominal CS (mm): 2.00
Defocus max (nm): 2,000.00
Defocus min (nm): 2,000.00
Tilt max (degrees): 60.00
Tilt min (degrees): -60.00
Holder model: SIDE ENTRY, EUCENTRIC
Acquisition
Number of images: 9
Sampling interval (μm): 15.0
Details: The dataset consists of 9 tomograms (containing 38 liposomes with bound gB). Data were binned by factor of 2.

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 1.00
Buffer: PBS with sodium citrate
Specimen support: Cflat
Vitrification
Apparatus: OTHER
Cryogen: ETHANE-PROPANE MIXTURE
Protocol: Blot manually for 3 s before plunging