3JBQ | pdb_00003jbq

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 of monoclonal antibody ROS-1
Sample Components
Rod cGMP-specific 3',5'-cyclic phosphodiesterase
Fab fragment of monoclonal antibody ROS-1

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	Applied 3 uL of 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 21100 particles were picked from ice images and CTF-corrected using Ctfit. Initial three-dimensional models were generated from either refe ...	A total of 21100 particles were picked from ice images and CTF-corrected using Ctfit. Initial three-dimensional models were generated from either reference-free class averages or from a cylinder. The two models were essentially similar. Three noise-seeded models were generated and used as initial models in Multirefine. A model with two Ros-1 Fabs bound emerged from a population of 15000 particles and was subjected to further refinement using standard iterative projection matching, class averaging, and Fourier reconstruction. The final three-dimensional map with C2 symmetry was generated from 12373 particles.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (3DBA, 3IBJ, 3JWR, 3JWR, 12E8, 12E8)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--rigid body refinement DETAILS--The domains were fit using Chimera. The model was refined using Phenix real-space refinement.

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	PHENIX
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	by particle using 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.