7QHB | pdb_00007qhb

Active state of GluA1/2 in complex with TARP gamma 8, L-glutamate and CTZ

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6QKC
experimental model	PDB	3TKD

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.477
f_angle_d	0.996
f_chiral_restr	0.067
f_bond_d	0.018
f_plane_restr	0.006

Sample
Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3-4 second blots

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	83344
Reported Resolution (Å)	3.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (6QKC, 3TKD)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial fitting was performed in Chimera with the Rigid Body fit option. The crystal structure of the L-Glu+CTZ GluA2 LBD was used for the LBD layer. After rigid body fitting Refmac and Phenix were used in refinement. Manual model building was performed in Coot

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	51

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	340
Maximum Defocus (nm)	2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
CTF CORRECTION	RELION
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	REFMAC
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	CTF refinement was performed after 3D reconstruction