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Nipah Virus Matrix Lattice in Complex with Human Cell Membrane
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
Henipavirus nipahense
Specimen Preparation
Sample Aggregation State
3D ARRAY
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SUBTOMOGRAM AVERAGING
Number of Particles
9767
Reported Resolution (Å)
7
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
CC
Overall B Value
351
Fitting Procedure
Details
The initial model of 1 M Dimer was generated with AlphaFold2. Model was docked into map in Chimera v1.1.4. RealSpaceRefine in Phenix of 1 M Dimer. Ope ...
The initial model of 1 M Dimer was generated with AlphaFold2. Model was docked into map in Chimera v1.1.4. RealSpaceRefine in Phenix of 1 M Dimer. Open refined model and map in Chimera. Duplicate model, rotate and dock. Re run RealSpaceRefine. Repeat for all dimers present in electron density map. Run comprehensive validation in Phenix which resulted in Ramachandran outliers of 0%, Allowed 7% and Favored of 93% .
We then removed all side chains from model prior to PDB deposition since our map does not support any side chain density - only backbone.