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High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.

by helical reconstruction, at 4.4 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2, Image by UCSF CHIMERA

#3: Simplified surface model with fitted atomic model: PDB-2om3, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1316
TitleHigh-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
MapA 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
SampleTobacco Mosaic Virus
AuthorsSachse C, Chen JZ, Coureux PD, Stroupe ME, Fandrich M, Grigorieff N
DateDeposition: 2007-01-22, Header release: 2007-01-22, Map release: 2007-06-25, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2, Image by UCSF CHIMERA

#3: Simplified surface model with fitted atomic model: PDB-2om3, Image by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-2om3

CiteFit

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Fit: output model of fitting

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Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 371, Issue 3, Page 812-35, Year 2007
TitleHigh-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
AuthorsCarsten 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.
KeywordsCryoelectron 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)
LinksPII: S0022-2836(07)00759-0, DOI: 10.1016/j.jmb.2007.05.088, PubMed: 17585939, PMC: PMC2025690
Map
Fileemd_1316.map.gz ( map file in CCP4 format, 31251 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.163 A/pix
= 232.6 A
200 pix
1.163 A/pix
= 232.6 A
200 pix
1.163 A/pix
= 232.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.581, 2 (movie #1):
Minimum - Maximum: -5.16884 - 6.75695
Average (Standard dev.): -0.0334474 (0.671369)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
Unit CellA= B= C: 232.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.163 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.1631.1631.163
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z232.600232.600232.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5.1696.757-0.033
Annotation DetailsA 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
Sample
NameTobacco Mosaic Virus
Number of Components1
Theoretical Mass37.5MDa
Component #1: virus - Virus
Scientific nameTobacco mosaic virus
Common NameVirus
Experimental Mass37.5 MDa
Scientific Name of SpeciesTobacco mosaic virus
Common Name of SpeciesVirus
NCBI taxonomy12242
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 4097
Host Species: Nicotiana tabacum
Host Category: PLANTAE(HIGHER PLANTS)
Experiment
Sample Preparation
Specimen Conc2.5 mg/ml
Specimen Support DetailsQuantifoil grid
Helical ParametersAxial Symmetry: s
Hand: RIGHT HANDED
Specimen Statefilament
BufferDetails: Phosphate (5mM EDTA)
pH: 7.4
Vitrification
Cryogen NameETHANE
Temperature277.15 Kelvin
InstrumentHOMEMADE PLUNGER
MethodBlot for 2 seconds before plunging
DetailsVitrification instrument: self-built model
Imaging
MicroscopeFEI TECNAI F30
Date2005-11-22
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 59000, Calibrated: 60190
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 4500 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature93 K ( 93 - 93 K)
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Number of Digital Images6
Sampling Size7
Quant Bit Number8
ScannerZEISS SCAI
Processing
Methodhelical reconstruction
3D reconstruction
AlgorithmSIRT - iterative algebraic reconstruction methods
SoftwareSpider
CTF CorrectionCTFFIND and CTFTILT phase-correction and amplitude-weighting of each paritcle after Grigorieff 1998
Resolution By Author4.4 A
Resolution Method5.0
DetailsFinal map was calculated from the central 241x241x241 cube.
Atomic Model Fitting
Model #0
Refinement Protocolflexible
Target Criteriaminimization of of least-square difference between observed and calculated densities
SoftwareXPLOR
Temperature factor90
Refinement SpaceREAL
DetailsProtocol: Torsion angle dynamics. 2TMV pdb code structure was adjusted to fit the density for residues 88-109 and refined
PDB Chain ID2OM3_A, and, 2OM3_R
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1316.xml (8.6 KB)
Map dataemd_1316.map.gz (8.6 MB)
Images1316.gif (60 KB)
FTP directoryftp://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