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.
Cryo-EM structure of the closed NF449-bound human P2X1 receptor
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
P51575
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
9.8889
f_angle_d
0.6784
f_chiral_restr
0.0445
f_plane_restr
0.0031
f_bond_d
0.0017
Sample
P2X1 receptor trimer
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK III
Cryogen Name
ETHANE
Sample Vitrification Details
Grids were frozen in liquid ethane using a Vitrobot Mark III operated at 4 degrees Celsius and 100% humidity with 12 blot force and 2 seconds blot tim ...
Grids were frozen in liquid ethane using a Vitrobot Mark III operated at 4 degrees Celsius and 100% humidity with 12 blot force and 2 seconds blot time.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
41932
Reported Resolution (Å)
2.61
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
RIGID BODY FIT
Refinement Target
Overall B Value
72.9
Fitting Procedure
Details
Initial fitting was performed in Chimerax and then refinements were performed in Coot and Phenix.
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
60
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
500
Maximum Defocus (nm)
1500
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
105000
Calibrated Magnification
105000
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Initial grid screening was conducted using a 200kV TFS Artica cryo-electron microscope prior to imaging on a Titan Krios cryo-electron microscope.
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
1.4
CTF CORRECTION
cryoSPARC
1.4
MODEL FITTING
Coot
0.9.8.92
MODEL REFINEMENT
PHENIX
1.20.1
INITIAL EULER ASSIGNMENT
cryoSPARC
1.4
FINAL EULER ASSIGNMENT
cryoSPARC
1.4
CLASSIFICATION
cryoSPARC
1.4
RECONSTRUCTION
cryoSPARC
1.4
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF correction was initially conducted on the set of motion-corrected images, with subsequent local CTF corrections applied to the final subset of particles.