Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Cryo-EM structure of TypeI tau filaments extracted from the brains of individuals with Corticobasal degeneration
ELECTRON MICROSCOPY
Sample
Tau filaments extracted from the Frontal cortex of a patient with corticobasal degeneration.
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Blot force: -12 ; Blot time: 4s
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
24073
Reported Resolution (Å)
3.2
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C1
Axial Rise
4.786
Angular Rotation
-0.845
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Fourier shell correlation
Overall B Value
26.63
Fitting Procedure
Details
A stack of three consecutive monomers was refined to preserve nearest-neighbour interactions for the middle chain. Because most residues adopted cross ...
A stack of three consecutive monomers was refined to preserve nearest-neighbour interactions for the middle chain. Because most residues adopted cross strand conformation, hydrogen-bond restraints were imposed to preserve a parallel, in-register hydrogen bonding pattern in earlier stages of Fourier-space refinements. Local symmetry restraints were imposed to keep all beta strand rungs identical. Side-chain clashes were detected using MOLPROBITY, and corrected by iterative cycles of real-space refinement in COOT and Fourier-space refinement in REFMAC and PHENIX. For each refined structure, separate model refinements were performed against a single half-map, and the resulting model was compared to the other half-map to confirm the absence of overfitting.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
1.346
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1700
Maximum Defocus (nm)
2800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
3.0
IMAGE ACQUISITION
EPU
1.10.0.77REL
CTF CORRECTION
CTFFIND
4.1
MODEL FITTING
Coot
0.8.9.1
INITIAL EULER ASSIGNMENT
RELION
3.0
FINAL EULER ASSIGNMENT
RELION
3.0
CLASSIFICATION
RELION
3.0
RECONSTRUCTION
RELION
3.0
MODEL REFINEMENT
REFMAC
5.8.0256
MODEL REFINEMENT
PHENIX
dev-2919
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
Aligned, non-dose-weighted micrographs were used to estimate the contrast transfer function (CTF) using CTFFIND4.1