EMDB-1316: High-resolution electron microscopy of helical specime...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1316
Authors	Sachse C, Chen JZ, Coureux PD, Stroupe ME, Fandrich M, Grigorieff N
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 2, Made by UCSF CHIMERA #3: Simplified surface model with fitted atomic model: PDB-2om3, Made by Jmol
Supplemental images	1316.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-2om3 CiteFit Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1766 PDB-4av2 PDB-1i84 List of similar structure data about Omokage system

Article
Citation - Primary
Article	J. Mol. Biol., Vol. 371, Issue 3, Page 812-35, Year 2007
Title	High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
Authors	Carsten Sachse, James Z Chen, Pierre-Damien Coureux, M Elizabeth Stroupe, Marcus Fändrich, Nikolaus Grigorieff Howard Hughes Medical Institute, Brandeis University - MS029, 415 South Street, Waltham, MA 02454, USA.
Keywords	Cryoelectron Microscopy, Hydrogen Bonding, Models, Biological, Models, Molecular, Protein Structure, Secondary, RNA, Viral (chemistry), Reproducibility of Results, Static Electricity, Tobacco Mosaic Virus (ultrastructure), Viral Proteins (chemistry), Virion (ultrastructure)
Links	PII: S0022-2836(07)00759-0, DOI: 10.1016/j.jmb.2007.05.088, PubMed: 17585939, PMC: PMC2025690

Map

File

EMD-1316.map ( map file in CCP4 format, 32001 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	0.581, 2 (movie #1):
Minimum - Maximum:	-5.16884 - 6.75695
Average (Standard dev.):	-0.0334474 (0.671369)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	200	200	200
Origin :	-100	-100	-100
Limit :	99	99	99
Spacing :	200	200	200

Unit Cell

A = 232.6 A , B = 232.6 A , C = 232.6 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 1.163 A , Y = 1.163 A , Z = 1.163 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	1.163	1.163	1.163
M x/y/z	200	200	200
origin x/y/z	0.000	0.000	0.000
length x/y/z	232.600	232.600	232.600
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-150	-150	-149
NX/NY/NZ	300	300	300
MAP C/R/S	1	2	3
start NC/NR/NS	-100	-100	-100
NC/NR/NS	200	200	200
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-5.169	6.757	-0.033

Annotation Details

A 69 Angstrom section of the virus. The complete virus contains contains approximately 44 repeats of this 69 Angstrom section. The section contains 49 asymmetric units of the helical virus.Cube of 241 x 241 x 241 Angstrom

Supplement
Images
Images	1316.gif

Sample
Name	Tobacco Mosaic Virus
Number of Components	1
Theoretical Mass	37.5 MDa
Component #1: virus - Virus
Scientific name	Tobacco mosaic virus
Common Name	Virus
Experimental Mass	37.5 MDa
Scientific Name of Species	Tobacco mosaic virus (NCBI Taxonomy: 12242)
Common Name of Species	Virus
Empty	No
Enveloped	No
Isolate	STRAIN
Class	VIRION
Natural Source	Host Species: Nicotiana tabacum (NCBI Taxonomy: 4097) Host Category: PLANTAE(HIGHER PLANTS)

Experiment
Sample Preparation
Specimen Conc	2.5 mg/ml
Specimen Support Details	Quantifoil grid
Helical Parameters	Axial Symmetry: s Hand: RIGHT HANDED
Specimen State	filament
Buffer	Details: Phosphate (5mM EDTA) pH: 7.4
Vitrification
Cryogen Name	ETHANE
Temperature	277.15 Kelvin
Instrument	HOMEMADE PLUNGER
Method	Blot for 2 seconds before plunging
Details	Vitrification instrument: self-built model
Imaging
Microscope	FEI TECNAI F30
Date	2005-11-22
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	15 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 59000 X, Calibrated: 60190 X
Astigmatism	objective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	1500 nm - 4500 nm
Specimen Holder
Holder	Side entry liquid nitrogen-cooled cryo specimen holder ( GATAN LIQUID NITROGEN )
Tilt Angle	0 degrees - 0 degrees
Temperature	93 Kelvin ( 93 Kelvin - 93 Kelvin )
Camera
Detector	Kodak ISO153 film
Image Acquisition
Number of Digital Images	6
Sampling Size	7.0 microns
Quant Bit Number	8
Scanner	ZEISS SCAI

Processing
Method	helical reconstruction
3 D reconstruction
Algorithm	SIRT - iterative algebraic reconstruction methods
Software	Spider
CTF Correction	CTFFIND and CTFTILT phase-correction and amplitude-weighting of each paritcle after Grigorieff 1998
Resolution By Author	4.4
Resolution Method	5.0
Details	Final map was calculated from the central 241x241x241 cube.
Atomic Model Fitting
Model #0
Refinement Protocol	flexible
Target Criteria	minimization of of least-square difference between observed and calculated densities
Software	XPLOR
Temperature factor	90
Refinement Space	REAL
Details	Protocol: Torsion angle dynamics. 2TMV pdb code structure was adjusted to fit the density for residues 88-109 and refined
Fitted Coordinate
PDB entry ID	PDB-2om3

Download

Data from EMDB

Header (meta data in XML format)

emd-1316.xml (8.6 KB)

Map data

emd_1316.map.gz (8.6 MB)

Images

1316.gif (60 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1316

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 5.3 MB Session file for UCSF-Chimera, 26.4 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 5.1 MB Session file for UCSF-Chimera, 26.4 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.2 MB