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)
TypeSourceAccession CodeDetails
experimental modelPDB 2IZX 
experimental modelPDB 2VFL 
experimental modelPDB 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 StatePARTICLE
Staining TypeNEGATIVE
Staining MaterialUranyl Formate
Staining Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1000
Reported Resolution (Å)35
Resolution MethodFSC 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 TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (2IZX, 2IZX)2 (2VFL)3 (2QVS, 2QVS)
Refinement SpaceREALREALREAL
Refinement ProtocolRIGID BODY FITRIGID BODY FITRIGID BODY FIT
Refinement Targetcross-correlationcross-correlationcross-correlation
Overall B Value
Fitting Procedure
DetailsREFINEMENT 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 TypeGENERIC GATAN
Electron Dose (electrons/Å**2)15
Imaging Experiment1
Date of Experiment2012-05-01
Temperature (Kelvin)298
Microscope ModelFEI TECNAI 12
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)50
Nominal CS6.3
Imaging ModeBRIGHT FIELD
Specimen Holder ModelOTHER
Nominal Magnification52000
Calibrated Magnification
SourceLAB6
Acceleration Voltage (kV)120
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONIMAGIC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
Each Micrograph