1P58

Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction

ELECTRON MICROSCOPY

Starting Model(s)

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

Sample
DENGUE VIRUS

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Details	SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	1691
Reported Resolution (Å)	9.5
Resolution Method
Other Details	THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED ...	THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER AND CHENG, 1996, J.STRUC.BIOL. 116,120-130) AND REFINED BY THE MODEL-BASED FOURIER TRANSFORM REFINEMENT PROCEDURE(http://bond.cs.ucf.edu/ComputationalBiology/Projects/POR/Home.html).
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1SVB, 1JCH)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	27

Imaging Experiment	1
Date of Experiment	2000-06-27
Temperature (Kelvin)	87
Microscope Model	FEI/PHILIPS CM200T
Minimum Defocus (nm)	800
Maximum Defocus (nm)	4800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	50000
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*(1-\|CTF\|)]

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.