3JAB | pdb_00003jab

Domain organization and conformational plasticity of the G protein effector, PDE6

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DBA
experimental model	PDB	3IBJ
experimental model	PDB	3JWR
experimental model	PDB	12E8

Sample
Bovine rod PDE6 holoenzyme in complex with the Fab fragment from the ROS-1 monoclonal antibody
Sample Components
Rod cGMP-specific 3',5'-cyclic phosphodiesterase
monoclonal antibody Fab fragment of ROS-1

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	Applied 3 uL sample per grid and blotted for 1 second before plunging into liquid ethane (FEI VITROBOT MARK III).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	12373
Reported Resolution (Å)	11
Resolution Method	FSC 0.143 CUT-OFF
Other Details	A total of 21,100 particles were picked from ice images and CTF corrected using Ctfit. After an initial 3D model was generated as described for PDE6, ...	A total of 21,100 particles were picked from ice images and CTF corrected using Ctfit. After an initial 3D model was generated as described for PDE6, three noise-seeded models were generated and used as initial models in the Multirefine procedure. A model with two Ros-1 Fab bound with a population of ~15,000 particles emerged and was subjected to further refinement using standard iterative projection matching, class averaging, and Fourier reconstruction. The final 3D maps with C2 symmetry were generated from 12,373 particles.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	Refinement Space	Refinement Protocol	Refinement Target	Overall B Value	Fitting Procedure	Details
1 (3DBA)	REAL	RIGID BODY FIT				REFINEMENT PROTOCOL--rigid body DETAILS--Domains w ...	REFINEMENT PROTOCOL--rigid body DETAILS--Domains were separately fitted by manual docking and Fit in Map in Chimera. The fitting of GFA(A,B) was confirmed using Folderhunter.
2 (3IBJ)
3 (3JWR)
4 (3JWR)
5 (12E8)
6 (12E8)

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2011-08-08
Temperature (Kelvin)
Microscope Model	JEOL 2010F
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	60000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	Parallel beam illumination

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	EMAN ctfit

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.