3J5Q | pdb_00003j5q

Structure of TRPV1 ion channel in complex with DkTx and RTX determined by single particle electron cryo-microscopy

ELECTRON MICROSCOPY

Sample
Rat TRPV1 in complex with DkTx and resiniferatoxin

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III)

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	36158
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but ar ...	The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental density. Interatomic clashes between the ankyrin repeats and the C-terminal beta sheet are the result of poor geometry due to relatively poor experimental density in these regions. Resolution and averaging of DkTx density was insufficient to provide side chain geometry. The DkTx model was generated as a poly-ALA model based on hanatoxin (PDB entry 1D1H) and docked into the DkTx density with slight modification. (Single particle details: 3D classification, refinement, and reconstruction were performed using RELION) (Single particle--Applied symmetry: C4)
Refinement Type	HALF-MAPS REFINED INDEPENDENTLY
Symmetry Type	POINT
Point Symmetry	C4

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--de novo model building DETAILS--The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyr ...	REFINEMENT PROTOCOL--de novo model building DETAILS--The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental density.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	21

Imaging Experiment	1
Date of Experiment	2013-01-01
Temperature (Kelvin)
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	31000
Calibrated Magnification	31000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Gatan K2 Summit operated in super-resolution counting mode, image recorded with dose fractionation method.

EM Software
Task	Software Package	Version
RECONSTRUCTION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Each particle

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.