1Q5B

lambda-shaped TRANS and CIS interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography

ELECTRON MICROSCOPY

Sample
SKIN
Sample Components
desmosome

Specimen Preparation
Sample Aggregation State	TISSUE
Vitrification Instrument
Cryogen Name	NITROGEN
Sample Vitrification Details	high pressure frozen and freezing substituted with 1% OsO4/0.1% Ur-Ac. in acetone, LX-112 resin embeded sample. 50nm thin section

3D Reconstruction
Reconstruction Method	TOMOGRAPHY
Number of Particles
Reported Resolution (Å)	30
Resolution Method
Other Details	sectioned sample thickness 47.2 nm; +/- 75 degree dual-axis tilt-series with increment 1 degree, dual-axis electron tomography with IMOD. 1.169nm al ...	sectioned sample thickness 47.2 nm; +/- 75 degree dual-axis tilt-series with increment 1 degree, dual-axis electron tomography with IMOD. 1.169nm alignment error
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1L3W)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	best visual fit using the program AmiraMOL 3.0
Overall B Value
Fitting Procedure
Details	METHOD--tracking 3D density REFINEMENT PROTOCOL--rigid body

Data Acquisition
Detector Type	GENERIC GATAN
Electron Dose (electrons/Å**2)	1200

Imaging Experiment	1
Date of Experiment	2002-11-23
Temperature (Kelvin)	295
Microscope Model	FEI/PHILIPS CM200FEG
Minimum Defocus (nm)	300
Maximum Defocus (nm)	500
Minimum Tilt Angle (degrees)	-78
Maximum Tilt Angle (degrees)	79
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	50000
Calibrated Magnification	68276
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	Dose is for whole dataset, not individual images

EM Software
Task	Software Package	Version
RECONSTRUCTION	IMOD
MODEL FITTING	Amira	3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	no CTF correction. Imaging at underfocus 0.4 micron with CM200FEG microscope at 50,000 magnification

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.