1LD4

Placement of the Structural Proteins in Sindbis Virus

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SVB
experimental model	PDB	1YSA
experimental model	PDB	1I9W

Sample
Sindbis Virus

Specimen Preparation
Sample Aggregation State	PARTICLE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)	11.4
Resolution Method
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1SVB, 1YSA, 1I9W)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value	1000
Fitting Procedure
Details	DETAILS--The structure of the lipid-enveloped Sindbis virus has been determined by fitting atomic resolution crystallographic structures of component proteins into an 11 resolution cryo- electron microscopy (cryoEM) map (with significant terms to 10 resolution). The E1 glycoprotein, whose structure had been determined independently for the homologous Semliki Forest virus by X-ray crystallography (Lescar, J., Roussel,A., Wein, M.W., Navaza, J., Fuller, S.D., Wengler, G., and Rey, F.A. (2001). The fusion glycoprotein shell of Semliki Forest virus- an icosahedral assembly primed for fusogenic activation at endosomal pH. Cell 105, 137-148), was fitted into the cryoEM density, in part by using the known positions of glycoprotein sites as restraints. The well-resolved transmembrane regions form coiled coils that could be fitted with the dimeric GCN4 coiled-coil structure. The helices could be seen to extend to E1 and E2 on the outside of the membrane and to the nucleocapsid on the inside. The known structure of the capsid protein (Choi, H.K., Tong, L., Minor, W., Dumas, P., Boege, U., Rossmann, M.G., and Wengler, G. (1991). Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Nature 354, 37-43.) was fitted into the density corresponding to the nucleocapsid, revising an earlier published structure.

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	18.4

Imaging Experiment	1
Date of Experiment	2000-06-15
Temperature (Kelvin)	87
Microscope Model	FEI/PHILIPS CM200T
Minimum Defocus (nm)	1100
Maximum Defocus (nm)	2580
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	38000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	EMfit
RECONSTRUCTION	EM3DR

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	each viral image was CTF corrected before reconstruction, based on the following equation: F(corr)=F(obs)/[|CTF|+wiener]