3J4Q

Pseudo-atomic model of the AKAP18-PKA complex in a bent conformation derived from electron microscopy

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IZX
experimental model	PDB	2VFL
experimental model	PDB	2QVS

Sample
AKAP18-PKA Complex in Bent Conformation
Sample Components
A-Kinase Anchoring Protein 18
A-Protein Kinase Regulatory Subunit II alpha
A-Protein Kinase Catalytic Subunit

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	1000
Reported Resolution (Å)	35
Resolution Method	FSC 0.5 CUT-OFF
Other Details	(Single particle details: Images were processed in IMAGIC and ISAC. 3D reconstruction was done in IMAGIC and FREALIGN.) (Single particle--Applied sym ...	(Single particle details: Images were processed in IMAGIC and ISAC. 3D reconstruction was done in IMAGIC and FREALIGN.) (Single particle--Applied symmetry: C1)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (2IZX, 2IZX)	2 (2VFL)	3 (2QVS, 2QVS)
Refinement Space	REAL	REAL	REAL
Refinement Protocol	RIGID BODY FIT	RIGID BODY FIT	RIGID BODY FIT
Refinement Target	cross-correlation	cross-correlation	cross-correlation
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--rigid body DETAILS--This domain was linked to the AKAP18 central domain (PDB 2VFL) using COOT and they were fit together into th ...	REFINEMENT PROTOCOL--rigid body DETAILS--This domain was linked to the AKAP18 central domain (PDB 2VFL) using COOT and they were fit together into the EM density.	REFINEMENT PROTOCOL--rigid body DETAILS--This domain was linked to the AKAP RII Binding Domain (PDB 2IZX) using COOT and they were fit together into ...	REFINEMENT PROTOCOL--rigid body DETAILS--This domain was linked to the AKAP RII Binding Domain (PDB 2IZX) using COOT and they were fit together into the EM density.	REFINEMENT PROTOCOL--rigid body DETAILS--This domain was linked to the PKA RIIalpha D/D domain (PDB 2IZX) using COOT and they were fit together into ...	REFINEMENT PROTOCOL--rigid body DETAILS--This domain was linked to the PKA RIIalpha D/D domain (PDB 2IZX) using COOT and they were fit together into the EM density.

Data Acquisition
Detector Type	GENERIC GATAN
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2012-05-01
Temperature (Kelvin)	298
Microscope Model	FEI TECNAI 12
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)	50
Nominal CS	6.3
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	52000
Calibrated Magnification
Source	LAB6
Acceleration Voltage (kV)	120
Imaging Details

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

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