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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

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-5369
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EMDB-5372
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Cite: data citing same article

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Diagram

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EMDB-5283

EMDB-2027

EMDB-2060

EMDB-5380
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, 7440-70-2), Capsid (metabolism), Capsid Proteins (genetics), Cations, Divalent (metabolism), Cryoelectron Microscopy, Image Processing, Computer-Assisted, Magnesium (metabolism, 7439-95-4), 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 ( map file in CCP4 format, 67110 KB )
Projections & SlicesSize of images:
AxesZ (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:7.0 (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 Order : X Y Z
Dimensions : 256 256 256
Origin : -128 -128 -128
Limit : 127 127 127
Spacing : 256 256 256
Unit CellA = 504.32 A , B = 504.32 A , C = 504.32 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 1.97 A , Y = 1.97 A , 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
Sample
NameRCNMV
Number of Components1
Theoretical Mass7 MDa
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 (NCBI Taxonomy: 12267)
Common Name of SpeciesRCNMV
EmptyNo
EnvelopedNo
IsolateSPECIES
ClassVIRION
Natural SourceHost Species: Dianthus (NCBI Taxonomy: 3569)
Host Category: PLANTAE(HIGHER PLANTS)
ShellDiameter: 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 X, Calibrated: 49523 X
Astigmatismmanual
Nominal Cs2.0 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 2800 nm
Specimen Holder
HolderGATAN 626 ( GATAN LIQUID NITROGEN )
Tilt Angle0 degrees - 0 degrees
Temperature95 Kelvin ( 95 Kelvin - 123 Kelvin )
Camera
DetectorKodak SO163 film
Image Acquisition
Od Range1.5
ScannerZEISS SCAI
Number of Digital Images1000
Sampling Size7 microns
Quant Bit Number16
Processing
Methodsingle particle (icosahedral) reconstruction
3 D reconstruction
AlgorithmPFT
SoftwarePFT
CTF Correctionmicrograph
Resolution By Author16.5
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections4000
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
DetailsProtocol: NNM
SoftwareSITUS
Refinement SpaceREAL
Download
Data from EMDB
Header (meta data in XML format)emd-5373.xml (8 KB)
Map dataemd_5373.map.gz (60.5 MB)
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