Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution
Sample Components
Cryo-EM map of the yeast Exocyst complex head-part structure at 6.7A resolution
Cryo-EM map of the yeast Exocyst complex top head-part structure at 6.2A resolution
Cryo-EM map of the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
Cryo-EM map of the yeast Exocyst complex body-part structure at 4.4A resolution
Cryo-EM map mask for the Yeast Exocyst complex overall structure at 5.5A resolution
Cryo-EM map mask for the Yeast Exocyst complex head structure at 6.7A resolution
Cryo-EM map mask for the yeast Exocyst complex top head-part structure at 6.2A resolution
Cryo-EM map mask for the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
Cryo-EM map mask for the yeast Exocyst complex body-part structure at 4.4A resolution
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Protein sample was applied onto a Quantifoil R1.2/1.3 golden grid and hold for 60 seconds, then blot for 2.5 seconds before plunging.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
343342
Reported Resolution (Å)
4.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
1 (2B1E)
REAL
RIGID BODY FIT
Exo70 (a.a.67-623) was first fit into the map with ...
Exo70 (a.a.67-623) was first fit into the map with Situs as a rigid body. Then it was split as Exo70 (a.a.67-344) and Exo70 (a.a.345-623), and fit into the same position with Chimera.
2 (2D2S)
REAL
RIGID BODY FIT
Well fit by one step Situs fitting.
3 (2FJI)
REAL
RIGID BODY FIT
The fitting position of this chain was determined ...
The fitting position of this chain was determined by cross-link mass spectrum.
4 (5H11)
REAL
RIGID BODY FIT
The yeast Sec10 (a.a.234-867) model was first obta ...
The yeast Sec10 (a.a.234-867) model was first obtained with Swiss-Model prediction based on this zebrafish originated initial model, and then fit into the map. Local adjustment was made with Coot. Final refinement was proceeded with Phenix real-space refinement.
5 (1ZC4)
REAL
RIGID BODY FIT
The yeast Exo84 (a.a.346-470) model was first obta ...
The yeast Exo84 (a.a.346-470) model was first obtained with PHYRE2 prediction based on this rat originated initial model, and then fit into the map. Final refinement was proceeded with Phenix real-space refinement.
6 (2A2F)
REAL
RIGID BODY FIT
The yeast Sec15 (a.a.482-896) model was first obta ...
The yeast Sec15 (a.a.482-896) model was first obtained with PHYRE2 prediction based on this Drosophila originated initial model, and then fit into the map. Local adjustment was made with Coot. Final refinement was proceeded with Phenix real-space refinement.
7 ()
REAL
BACKBONE TRACE
All remaining models were manually built as backbo ...
All remaining models were manually built as backbone tracing Poly-Alanine, yet the present residues are shown as original. The backbone trace was guided by the EM map connectivity, secondary structure prediction and cross-link mass spectrum. The model was validated with different sets of cross-link mass spectrum data to confirmed the correctness.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
2000
Maximum Defocus (nm)
3000
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
22500
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
1.4
IMAGE ACQUISITION
UCSFImage
4
CTF CORRECTION
RELION
1.4
MODEL FITTING
Situs
2.8
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Situs
2.8
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
Coot
0.8.2
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
Coot
0.8.2
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Coot
0.8.2
MODEL REFINEMENT
PHENIX
1.11.1
INITIAL EULER ASSIGNMENT
RELION
1.4
FINAL EULER ASSIGNMENT
RELION
1.4
CLASSIFICATION
RELION
1.4
RECONSTRUCTION
RELION
1.4
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
The defocus value of each image was determined by CTFFIND3.