9BEI | pdb_00009bei

Cryo-EM structure of synthetic claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-2, and Nanobody

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7DTM
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.383
f_angle_d	0.734
f_chiral_restr	0.046
f_plane_restr	0.006
f_bond_d	0.003

Sample
Synthetic human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-2, and nanobody against COP-2

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	3.5 microL of complex was applied onto grids and blotted for 3 s at 4 degrees C under 100 percent humidity then plunge frozen into liquid ethane coole ...	3.5 microL of complex was applied onto grids and blotted for 3 s at 4 degrees C under 100 percent humidity then plunge frozen into liquid ethane cooled by liquid nitrogen.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	21296
Reported Resolution (Å)	4.16
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (7DTM, 7DTM, 7DTM)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value	322
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	49.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	400
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	120000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.4.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	4.4.1
MODEL FITTING	PHENIX	1.20.1-4487
MODEL REFINEMENT	PHENIX	1.20.1-4487
INITIAL EULER ASSIGNMENT	cryoSPARC	4.4.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.1
CLASSIFICATION	cryoSPARC	4.4.1
RECONSTRUCTION	cryoSPARC	4.4.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1848208