5IDF | pdb_00005idf

Cryo-EM structure of GluA2/3 AMPA receptor heterotetramer (model II)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HSY
experimental model	PDB	1FTO
experimental model	PDB	3UA8
experimental model	PDB	3O21
experimental model	PDB	3KG2

Sample
AMPA GluA2/3 heterotetramer

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Incubated for 1 minute, blotted for 3 seconds

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	14119
Reported Resolution (Å)	10.31
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (3HSY, 1FTO, 3UA8, 3O21, 3KG2)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	For GluA2 chains (A,C), 2 copies of GluA2 NTD (3HSY) and two copies of GluA2 LBD (1FTO) were fitted. For GluA3 chains (B,D), 2 copies of GluA3NTD (3O2 ...	For GluA2 chains (A,C), 2 copies of GluA2 NTD (3HSY) and two copies of GluA2 LBD (1FTO) were fitted. For GluA3 chains (B,D), 2 copies of GluA3NTD (3O21) and two copies of GluA2 LBD (3UA8) were fitted.For the TMD region, the 4 chains of 3KG2 TMD (residues 509-544 594-629 784-817) were fitted as a rigid body. After fitting the sequence was corrected including mutations and side chains were removed.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	4000
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	28409
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	EMAN	2
PARTICLE SELECTION	RELION
CTF CORRECTION	Gctf
MODEL FITTING	UCSF Chimera
INITIAL EULER ASSIGNMENT	RELION
FINAL EULER ASSIGNMENT	RELION
CLASSIFICATION	RELION
RECONSTRUCTION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		107939

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.