9KCH | pdb_00009kch

Cryo-EM structure of inner membrane TolQRA complex in CYMAL-6-Neopentyl Glycol detergent micelles

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	P0ABU9
in silico model	AlphaFold	P0ABV6
in silico model	AlphaFold	P19934

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.648
f_angle_d	0.764
f_chiral_restr	0.042
f_plane_restr	0.005
f_bond_d	0.004

Sample
Inner membrane TolQRA complex in detergent micelles
Sample Components
Pentameric complex of inner membrane Tol-Pal system protein TolQ
Dimeric complex of inner membrane Tol-Pal system protein TolR

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	54048
Reported Resolution (Å)	4.19
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value	124.3
Fitting Procedure
Details	Building of the high-resolution structures of TolQRA was done via approximate fitting of each monomer independently using the Alphafold 3 model of Tol ...	Building of the high-resolution structures of TolQRA was done via approximate fitting of each monomer independently using the Alphafold 3 model of TolQ, TolR(TM), TolA(TM) as rigid bodies into the density in Chimera, followed by refinement in COOT.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	56

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2000
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
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.5.2
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC	4.5.2
MODEL FITTING	UCSF Chimera	1.15
MODEL FITTING	Coot	0.8.9
INITIAL EULER ASSIGNMENT	cryoSPARC	4.5.2
FINAL EULER ASSIGNMENT	cryoSPARC	4.5.2
CLASSIFICATION	cryoSPARC	4.5.2
RECONSTRUCTION	cryoSPARC	4.5.2
MODEL REFINEMENT	PHENIX	1.20.1-4487

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF routine in cryoSPARC	2497487	We performed automated particle picking using Blob and Template Picker for initial template picking and final sampling respectively.

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.