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Mutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid.

by single particle (icosahedral) reconstruction, at 32 A resolution

Movie

Orientation:

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

#2: Surface view colored by radius, Surface level: 1, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1882
TitleMutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid.
MapThis is a surface-rendered view of a Bacteriophage MS2 virus-like particle composed of purified coat protein and genomic RNA
SampleBacteriophage MS2 virus-like particles assembled in vitro from purified MS2 coat protein and genomic RNA
KeywordsBacteriophage MS2, virus assembly, quasi-equivalence, ssRNA virus
AuthorsRolfsson O, Toropova K, Ranson NA, Stockley PG
DateDeposition: 2011-02-21, Header release: 2011-05-13, Map release: 2011-05-13, Last update: 2012-09-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

#2: Surface view colored by radius, Surface level: 1, Image 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

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Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 401, Issue 2, Page 309-22, Year 2010
TitleMutually-induced conformational switching of RNA and coat protein underpins efficient assembly of a viral capsid.
AuthorsOttar Rolfsson, Katerina Toropova, Neil A Ranson, Peter G Stockley
Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
KeywordsBase Sequence, Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, DNA Primers (genetics), Imaging, Three-Dimensional, Levivirus (chemistry), Models, Molecular, Nucleic Acid Conformation, Protein Conformation, RNA, Viral (chemistry), Recombinant Proteins (chemistry), Virus Assembly (physiology)
LinksPubMed: 20684044, PII: S0022-2836(10)00562-0, DOI: 10.1016/j.jmb.2010.05.058
Map
Fileemd_1882.map.gz ( map file in CCP4 format, 31251 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.87 A/pix
= 374. A
200 pix
1.87 A/pix
= 374. A
200 pix
1.87 A/pix
= 374. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1 (by emdb), 1 (movie #1):
Minimum - Maximum: -4.45316 - 5.72175
Average (Standard dev.): 5.57511e-09 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
Unit CellA= B= C: 374 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.87 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.871.871.87
M x/y/z200200200
origin x/y/z-0.000-0.000-0.000
length x/y/z374.000374.000374.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-4.4535.7220.000
Annotation DetailsThis is a surface-rendered view of a Bacteriophage MS2 virus-like particle composed of purified coat protein and genomic RNA
Supplement
Images
Images
Sample
NameBacteriophage MS2 virus-like particles assembled in vitro from purified MS2 coat protein and genomic RNA
Number of Components2
Oligomeric StateOne capsid to one RNA
Component #1: virus - MS2
Scientific nameEnterobacterio phage MS2
Common NameMS2
Scientific Name of SpeciesEnterobacterio phage MS2
Common Name of SpeciesMS2
NCBI taxonomy12022
EnvelopedNo
EmptyNo
ClassVIRUS-LIKE PARTICLE
IsolateSTRAIN
Natural SourceHost Category: BACTERIA(EUBACTERIA)
NCBI taxonomy: 562
Host Species: Escherichia coli
ShellID: 1 , T Number: 3 , Diameter: 280 A
Component #2: nucleic-acid - Single stranded RNA MS2 genome
Scientific nameSingle stranded RNA MS2 genome
DetailsSingle stranded RNA MS2 genome was phenol-chloroform extracted from wild type MS2 phage
Scientific Name of SpeciesEnterobacteria phage MS2
Common Name of SpeciesMS2
NCBI taxonomy329852
ClassRNA
StructureSINGLE STRANDED
SyntheticNo
Experiment
Sample Preparation
Specimen Support DetailsQuantifoil R2/1 200 mesh holly carbon grid
Specimen Stateparticle
BufferDetails: 50mM Tris-acetate, 1mM magnesium acetate, 40mM ammonium acetate
pH: 7.6
Vitrification
Method1.6s blot
Cryogen NameETHANE
DetailsVitrification instrument: Double-sided custom pneumatic blotter
InstrumentHOMEMADE PLUNGER
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose18 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 52750
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderSide entry
ModelGATAN LIQUID NITROGEN
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerOTHER
Sampling Size9.88
Quant Bit Number16
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareSpider
CTF CorrectionPhase flip each particle
Resolution By Author32 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections80
Number of Class Averages19
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-1882.xml (7.8 KB)
Map dataemd_1882.map.gz (18.6 MB)
Imagesemd1882.jpg (171.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1882
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.6 KB