3J41 | pdb_00003j41

Pseudo-atomic model of the Aquaporin-0/Calmodulin complex derived from electron microscopy

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B6P
experimental model	PDB	1NWD

Sample
Aquaporin-0 bound to Calmodulin
Sample Components
Aquaporin-0
Calmodulin

Specimen Preparation
Sample Aggregation State	PARTICLE
Staining Type	NEGATIVE
Staining Material	Uranyl Formate
Staining Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	11720
Reported Resolution (Å)	25
Resolution Method	FSC 0.5 CUT-OFF
Other Details	Final Map with C2 Symmetry and Filtered to 25 Angstrom (Single particle details: Particles were selected from a tilted pair dataset at 0 and 50 degree ...	Final Map with C2 Symmetry and Filtered to 25 Angstrom (Single particle details: Particles were selected from a tilted pair dataset at 0 and 50 degree tilt using SPIDER. An initial reconstruction was generated using random conical tilt methods in SPIDER and refined in FREALIGN.) (Single particle--Applied symmetry: C2)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (2B6P, 1NWD)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	cross-correlation
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--rigid body DETAILS--A complete model of AQP0-CaM was built by fitting 2B6P and 1NWD into the EM map in Chimera. Loops connecting ...	REFINEMENT PROTOCOL--rigid body DETAILS--A complete model of AQP0-CaM was built by fitting 2B6P and 1NWD into the EM map in Chimera. Loops connecting the two structures were built using COOT and the final model was energy minimized to remove steric clashes. The geometries of the modeled loops (AQP0 residues 222-227) were not refined due to lack of resolution in the experimental map.

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2010-02-25
Temperature (Kelvin)
Microscope Model	FEI TECNAI 12
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)	50
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	52000
Calibrated Magnification	52000
Source	LAB6
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTF-TILT, each micrograph

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.