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 6Z5J | pdb_00006z5j

Arrangement of the matrix protein M1 in influenza A/Hong Kong/1/1968 VLPs (HA,NA,M1,M2)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EA3 
Sample
Influenza A virus
Sample Components
Matrix protein 1
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSUBTOMOGRAM AVERAGING
Number of Particles14767
Reported Resolution (Å)8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (1EA3)
Refinement Space
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsMultiple copies of the M1 NTD crystal structure (PDB:1ea3) were fitted as rigid bodies into the EM map to understand the relative arrangement of M1 mo ...Multiple copies of the M1 NTD crystal structure (PDB:1ea3) were fitted as rigid bodies into the EM map to understand the relative arrangement of M1 monomers in the context of the matrix layer inside the virus
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)2.9
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)2000
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
VOLUME SELECTIONTOM
VOLUME SELECTIONMATLAB
VOLUME SELECTIONUCSF Chimera
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND
CTF CORRECTIONNOVACTF
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONNOVACTF
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF determination was performed using CTFFIND4. CTF correction was performed by 3D-CTF correction by CTF multiplication in NovaCTF.