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.
Monomeric Spike glycoprotein ectodomain from SARS-CoV-2 in complex with a neutralising antibody P008_60
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
blotted for 3 to 4 sec before plunging
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
166619
Reported Resolution (Å)
4.31
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Non Uniform refinement in cryoSPARC
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (7A92, 5WI9, 5WI9)
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Correlation coefficient
Overall B Value
81
Fitting Procedure
Details
The atomistic models of monomeric SARS-CoV-2 S1 protein and a Fab molecule, extracted from PDB entries 7A92 and 5WI9, were docked in the cryo-EM map ...
The atomistic models of monomeric SARS-CoV-2 S1 protein and a Fab molecule, extracted from PDB entries 7A92 and 5WI9, were docked in the cryo-EM map using Chimera. The NTD and the RBD of the spike subunit were replaced with the crystal structures from PDB entries 7B62 and 7OAO, respectively. Guided by the cryo-EM map, the model was adjusted and extended interactively in Coot and refined using phenix.real_space_refine.
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
700
Maximum Defocus (nm)
3600
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
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
Gautomatch
0.53
IMAGE ACQUISITION
EPU
CTF CORRECTION
Gctf
1.06
MODEL FITTING
UCSF Chimera
CLASSIFICATION
RELION
3.1
RECONSTRUCTION
cryoSPARC
2
MODEL REFINEMENT
PHENIX
4213
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
1740430
Initially, particles were picked with Gautomatch-v0.53 using 2D class averages of the trimeric spike, low-pass filtered to 20 A resolution, as templates. The resulting 1,740,430 particles, extracted in Relion-3.1 and binned to a pixel size of 4.4 A, were subjected to two rounds of reference-free 2D classification in cryoSPARC-2. 283,956 particles belonging to well-defined 2D classes were subjected to classification into twelve 3D classes in Relion-3.1. Neither the 2D nor 3D class averages of the trimeric spike revealed features attributable to a bound Fab molecule. Next, 3,772,722 particles were picked using 2D class averages of the dissociated spikes. Following two rounds of 2D classification in cryoSPARC-2, 753,837 particles, re-extracted with pixel size of 2.2 A, were subjected to 3D classification in Relion-3.1 into 9 classes using an initial model obtained by Ab-initio reconstruction in cryoSPARC-2. The procedure revealed a single well-defined 3D class containing 208,343 particles (27.4%) of S1 protein with a bound Fab molecule. The particles, re-extracted without binning (with a pixel size 1.1 A), were subjected to two rounds of 3D classification using Ab-initio reconstruction in cryoSPARC-2 with 2 classes and class similarity set to 0. At the end of each round, the most populated class was selected, resulting in the final set of 166,619 particles.