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Structural transitions in RCNMV revealing potential mechanism of RNA release (EDTA map)

by single particle (icosahedral) reconstruction, at 16.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 7, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 7, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5373
TitleStructural transitions in RCNMV revealing potential mechanism of RNA release (EDTA map)
Mapthis is EM map of native RCNMV with EDTA
SampleRCNMV
Keywordscryo-electron microscopy, virus, red clover necrotic mosaic virus
AuthorsSherman MB, Guenther RH, Tama F, Sit TL, Brooks CL, Mikhailov AM, Orlova EV, Baker TS, Lommel SA
DateDeposition: 2011-12-16, Header release: 2011-12-19, Map release: 2011-12-19, Last update: 2011-12-19
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 7, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 7, Made by UCSF CHIMERA

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

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Virol., Vol. 80, Issue 21, Page 10395-406, Year 2006
TitleRemoval of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release.
AuthorsMichael B Sherman, Richard H Guenther, Florence Tama, Tim L Sit, Charles L Brooks, Albert M Mikhailov, Elena V Orlova, Timothy S Baker, Steven A Lommel
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
KeywordsAmino Acid Sequence, Calcium (metabolism), Capsid (metabolism), Capsid Proteins (genetics), Cations, Divalent (metabolism), Cryoelectron Microscopy, Image Processing, Computer-Assisted, Magnesium (metabolism), Models, Molecular, Molecular Sequence Data, Multiprotein Complexes, RNA, Viral (genetics), Sequence Homology, Amino Acid, Species Specificity, Static Electricity, Tombusviridae (genetics)
LinksDOI: 10.1128/JVI.01137-06, PubMed: 16920821, PMC: PMC1641784
Map
Fileemd_5373.map.gz ( map file in CCP4 format, 65537 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.97 A/pix
= 504.32 A
256 pix
1.97 A/pix
= 504.32 A
256 pix
1.97 A/pix
= 504.32 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:7 (by emdb), 7 (movie #1):
Minimum - Maximum: -37.0139 - 40.041
Average (Standard dev.): 0.747076 (4.72365)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
Unit CellA= B= C: 504.32 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.97 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.971.971.97
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z504.320504.320504.320
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-37.01440.0410.747
Annotation Detailsthis is EM map of native RCNMV with EDTA
Supplement
Images
Images
Sample
NameRCNMV
Number of Components1
Theoretical Mass7MDa
Detailsmonodisperse sample
Component #1: virus - RCNMV
Scientific nameRed clover necrotic mosaic virus
Common NameRCNMV
Theoretical Mass7 MDa
Experimental Mass7 MDa
Scientific Name of SpeciesRed clover necrotic mosaic virus
Common Name of SpeciesRCNMV
NCBI taxonomy12267
EmptyNo
EnvelopedNo
IsolateSPECIES
ClassVIRION
Natural SourceNCBI taxonomy: 3569
Host Species: Dianthus
Host Category: PLANTAE(HIGHER PLANTS)
ShellID: 1 , Diameter: 366 A, T Number: 3
Experiment
Sample Preparation
Specimen Conc1 mg/ml
Specimen Support Details200 mesh Quantifoil
Specimen Stateparticle
BufferDetails: 10 mM Tris-HCl
pH: 6.5
Vitrification
Cryogen NameETHANE
DetailsVitrification instrument: cryo-plunger
InstrumentHOMEMADE PLUNGER
Temperature90 Kelvin
Imaging
MicroscopeFEI/PHILIPS CM300FEG/T
Date15-OCT-2003
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 47000, Calibrated: 49523
Astigmatismmanual
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 2800 nm
Specimen Holder
HolderGATAN 626
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature95 K ( 95 - 123 K)
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Od Range1.5
ScannerZEISS SCAI
Number of Digital Images1000
Sampling Size7
Quant Bit Number16
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmPFT
SoftwarePFT
CTF Correctionmicrograph
Resolution By Author16.5 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections4000
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
DetailsProtocol: NNM
SoftwareSITUS
Refinement SpaceREAL
PDB Entry ID2TBV
Download
Data from EMDB
Header (meta data in XML format)emd-5373.xml (8 KB)
Map dataemd_5373.map.gz (60.5 MB)
Imagesemd_5373_1.jpg (25.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5373
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.5 KB