9RMS | pdb_00009rms

GluA4 in complex with TARP-2, Resting II state, structure of TMD/LBD domains

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O3B
experimental model	PDB	4U2R
experimental model	PDB	9QDN

Sample
GluA4 in complex with TARP-2, Resting II state, structure of TMD/LBD domain

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	35082
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (4O3B, 4U2R, 9QDN, 9QDN)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	I performed fitting using Chimera for the TMD domain (previously modeled and individually deposited in the PDB), along with the following LBDs: LBD mo ...	I performed fitting using Chimera for the TMD domain (previously modeled and individually deposited in the PDB), along with the following LBDs: LBD monomers from GluA4G2 Resting I (PDB ID: 9QDN) were fitted into chains A and D, while PDB entry 4U2R (GluA2 LBD, apo state) and PDB entry 4O3B (GluA2, aspartate-bound) were fitted into chains B and C, respectively. B-factors were reset, GluA4 residues were substituted, water molecules were removed, and NBQX was introduced. Subsequently, rigid-body refinement was performed using Phenix.

Data Acquisition
Detector Type	GATAN K3 BIOCONTINUUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
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	RELION	5.0
MODEL REFINEMENT	PHENIX	1.19.2_4158:
RECONSTRUCTION	cryoSPARC	4.3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION

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.