9NQY | pdb_00009nqy

Nipah Virus Matrix Lattice in Complex with Human Cell Membrane


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Henipavirus nipahense
Specimen Preparation
Sample Aggregation State3D ARRAY
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSUBTOMOGRAM AVERAGING
Number of Particles9767
Reported Resolution (Å)7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCC
Overall B Value351
Fitting Procedure
DetailsThe 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.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)3.65
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)1500
Maximum Defocus (nm)3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification63000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
VOLUME SELECTIONDynamo1.1.532
IMAGE ACQUISITIONSerialEM4.0.1
CTF CORRECTIONCTFFIND4
MODEL FITTINGUCSF Chimera1.1.4
MODEL REFINEMENTPHENIX1.21_5207
FINAL EULER ASSIGNMENTRELION4.0 Tomo
RECONSTRUCTIONRELION4.0 Tomo
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION