7N0G

CryoEm structure of SARS-CoV-2 spike protein (S-6P, 1-up) in complex with sybodies (Sb45)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XKL
experimental model	PDB	7KGJ
experimental model	PDB	7B32

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.985
f_angle_d	0.506
f_chiral_restr	0.048
f_plane_restr	0.004
f_bond_d	0.003

Sample
Spike protein (S-6P) in complex with Synthetic nanobody (Sb45)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	214171
Reported Resolution (Å)	3.02
Resolution Method	FSC 0.143 CUT-OFF
Other Details	A series of "Ab-initio 3D reconstruction" dividing 2 or 4 subclasses to identify two forms of configurations of S-6P, i.e. one RBD up or two RBD up.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6XKL, 6XKL, 6XKL, 7KGJ, 7KGJ, 7B32)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Correlation Coefficient
Overall B Value	157
Fitting Procedure
Details	An initial model for S-6P was generated using PDB 6XKL and rigid body fitted into the map using Chimera. The RBD domain (334-528) and Sb45 are taken f ...	An initial model for S-6P was generated using PDB 6XKL and rigid body fitted into the map using Chimera. The RBD domain (334-528) and Sb45 are taken from 7KGJ which was superimposed onto the S-6P model in PyMol. The NTD domain (14-289) is taken from 7B32 with full sequence and replace that of 6XKL. We have rebuilt and added more glycans (NAGs). We used the real-space refinement in PHENIX including rigid-body refinement. RBD and NTD are subjected to rigid-body refinement. Simulate annealing (SA) runs once at the initial micro-step, local grid search and ADP refinements were included, using the secondary structure restraints.

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	56

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	2000
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	130000
Calibrated Magnification	47529
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v3.2.0
IMAGE ACQUISITION	SerialEM	3.8.0
CTF CORRECTION	cryoSPARC	v3.2.0
MODEL FITTING	UCSF Chimera	2021
MODEL REFINEMENT	PHENIX	1.19.2
CLASSIFICATION	cryoSPARC	3.2.0
RECONSTRUCTION	cryoSPARC	V3.2.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE	patch CTF estimation	1433963	A total of 9,725 micrographs were imported into cryoSPARC. Following patch Motion correction, patch CTF estimation, and curation, the number of micrographs was reduced to 9,237. The blob picker with the particle diameter between 128 and 256 angstroms was used for picking up particles. We used the box size of 400 pixels and extracted 1,433,963 particles initially.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.