EMDB-5296: cryo-EM reconstruction of West Nile virus

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5296
Authors	Zhang W, Kaufmann B, Chipman PR, Kuhn RJ, Rossmann MG
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 40, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 40, Made by UCSF CHIMERA
Supplemental images	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-3j0b CiteFit Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-5115 EMDB-1234 EMDB-5117 EMDB-1399 EMDB-1407 EMDB-5187 List of similar structure data about Omokage system

Article
Citation - Primary
Article	J. Struct. Biol., Year 2013
Title	Membrane curvature in flaviviruses.
Authors	Wei Zhang, Bärbel Kaufmann, Paul R Chipman, Richard J Kuhn, Michael G Rossmann Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States; Institute of Molecular Virology, Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, United States. Electronic address:
Links	PII: S1047-8477(13)00100-7, DOI: 10.1016/j.jsb.2013.04.005, PubMed: 23602814

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 752.25 A , B = 752.25 A , C = 752.25 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 2.95 A , Y = 2.95 A , Z = 2.95 A

CCP4 map header info

Annotation Details

This is a reconstruction map of West Nile virus

Sample
Name	West Nile Virus
Number of Components	3
Component #1: virus - West Nile Virus
Scientific name	West Nile virus
Common Name	West Nile Virus
Scientific Name of Species	West Nile virus (NCBI Taxonomy: 11082)
Common Name of Species	West Nile Virus
Empty	No
Enveloped	Yes
Isolate	STRAIN
Class	VIRION
Natural Source	Host Species: Homo sapiens (NCBI Taxonomy: 9606) Host Category: VERTEBRATES
Shell	Diameter: 500 A Name Element: E T Number: 1

Experiment
Sample Preparation
Staining	none
Specimen Support Details	400 mesh holey carbon grid
Specimen State	particle
Buffer	Details: 12 mM Tris-HCl,120 mM NaCl, 1 mM EDTA pH: 8.0
Vitrification
Cryogen Name	ETHANE
Details	vitrification carried out in a BSL3 lab
Instrument	NONE
Imaging
Microscope	FEI/PHILIPS CM300FEG/T
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	30 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Calibrated: 47440 X
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	112 nm - 321 nm
Specimen Holder
Holder	Eucentric ( GATAN LIQUID NITROGEN )
Tilt Angle	0.0 degrees - 0.0 degrees
Camera
Detector	Kodak SO163 film
Image Acquisition
Scanner	ZEISS SCAI
Number of Digital Images	83
Sampling Size	7 microns

Processing
Method	single particle (icosahedral) reconstruction
3 D reconstruction
Software	Auto3DEM
CTF Correction	each particle
Resolution By Author	10.3
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	1556
Applied Symmetry	I (icosahedral)
Atomic Model Fitting
Model #0
Details	Protocol: Rigid Body
Software	EMFIT
Refinement Protocol	rigid body
Refinement Space	REAL
Fitted Coordinate
PDB entry ID	PDB-3j0b

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.6 MB Session file for UCSF-Chimera, 27.1 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.1 MB .webm (WebM/VP8 format), 4.8 MB Session file for UCSF-Chimera, 27.1 KB