6TIK | pdb_00006tik

Hepatitis B virus core shell--virus-like particle with NadA epitope

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QGT

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.539
f_angle_d	0.8561
f_chiral_restr	0.0517
f_bond_d	0.008
f_plane_restr	0.0066

Sample
VLP fusion sequence expressed in E.coli.

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3 ul applied for 30s at room temperature, then 4 - 5 s blot

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	8598
Reported Resolution (Å)	3.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1QGT)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Correlation with the map plus geometry
Overall B Value	111.33
Fitting Procedure
Details	The 4 protein chains from the original T=4 HBV core shell structure solved by X-ray crystallography (Wynne, Leslie, Crowther, 1999), PDB code 1QGT, representing two independently resolved dimeric spikes, were docked into the map using DockEM, and visualised in UCSF Chimera. Part of the chains near the tips of the spikes did not fit well to the map. This region of the map, corresponding to the major immune dominant region where the inserted NadA epitope was placed, was poorly resolved. Therefore the model region according to the native sequence between, but not including, Leu76 to Arg82 was deleted from all 4 chains. This model was then refined against the map with the phenix.real_space_refine program, using global minimisation, simulated annealing, B-factor refinement, and without non-crystallographic symmetry (NCS) restraints. Default parameters were used for other constraints. The resulting model was re-refined once using the local_grid_search option, with all other parameters left unchanged.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	79

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	104167
Calibrated Magnification	100719
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	EMAN2	2.01
IMAGE ACQUISITION	EPU
CTF CORRECTION	EMAN2	2.01
MODEL FITTING	DockEM
MODEL REFINEMENT	PHENIX	PHENIX.real-space_refine
INITIAL EULER ASSIGNMENT	cryoSPARC	v0.65
FINAL EULER ASSIGNMENT	cryoSPARC	v0.65
CLASSIFICATION	cryoSPARC	v0.65
RECONSTRUCTION	cryoSPARC	v0.65

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		10119	Initially ~44,000 particles were initially picked and extracted in EMAN. Approx 12,000 were shell fragments or incomplete. Others were intact but lower resolution, so damaged or affected by charging, or other issue. After filtering/cleaning by EMAN2 2D classification 10119 particles were taken forwards for initial 3D reconstruction in EMAN2. This set of 10119 was then 2D cleaned by CryoSPARC to give 9145 particles.