Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Prefusion structure of a human coronavirus spike protein
ELECTRON MICROSCOPY
Sample
HKU1 spike with attached foldon domain and mutated furin-cleavage site
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
3 uL sample was applied to grid, blotted, and plunged into liquid ethane.
Staining Type
NEGATIVE
Staining Material
uranyl formate
Staining Details
3 uL sample was applied to grid for 30 seconds and then blotted. Grids were stained with 3 uL 1% uranyl formate for 60 seconds followed by blotting.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
31435
Reported Resolution (Å)
4.04
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C3
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
EMRinger
Overall B Value
117
Fitting Procedure
Details
Model building and refinement were conducted using a combination of software programs.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
57
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
22500
Calibrated Magnification
22500
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
DoG Picker
PARTICLE SELECTION
FindEM
IMAGE ACQUISITION
Leginon
CTF CORRECTION
CTFFIND3
MODEL FITTING
MODELLER
MODEL FITTING
Rosetta
2015.19
MODEL FITTING
Coot
0.8.2
INITIAL EULER ASSIGNMENT
RELION
1.3
FINAL EULER ASSIGNMENT
RELION
1.4b1
CLASSIFICATION
IMAGIC
RECONSTRUCTION
RELION
1.4b1
MODEL REFINEMENT
Rosetta
2015.19
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
39164
2188 particles were selected from a subset of the data using DoG Picker. These particles were used to generate a 3D model from which back projections were derived. Back projection images were used as templates for picking particles from the entire dataset using FindEM.