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Structure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis

by single particle reconstruction, at 23 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.04, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.04, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2073
AuthorsMuller DA, Landsberg MJ, Bletchly C, Rothnagel R, Waddington L, Hankamer B, Young PR
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.04, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.04, Made by UCSF CHIMERA

Supplemental images

emd_2073.jpg
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

EMDB-5220

EMDB-1270

EMDB-2332
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Gen. Virol., Vol. 93, Issue Pt 4, Page 771-9, Year 2012
TitleStructure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis.
AuthorsDavid A Muller, Michael J Landsberg, Cheryl Bletchly, Rosalba Rothnagel, Lynne Waddington, Ben Hankamer, Paul R Young
Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia.
KeywordsAnimals, Antigens, Viral (immunology), Cercopithecus aethiops, Dengue Virus (ultrastructure), Electrophoresis, Polyacrylamide Gel, Image Interpretation, Computer-Assisted, Microscopy, Electron, Transmission, NS1 protein, Dengue virus type 2, Protein Conformation, Recombinant Proteins, Vero Cells, Viral Nonstructural Proteins (immunology)
LinksDOI: 10.1099/vir.0.039321-0, PubMed: 22238236
Map
FileEMD-2073.map ( map file in CCP4 format, 5040 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:1.04 (by author), 1.04 (movie #1):
Minimum - Maximum: -3.19926310 - 6.28529167
Average (Standard dev.): 0.02490416 (0.49955314)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 108 108 108
Origin : -135 -135 -135
Limit : -28 -28 -28
Spacing : 108 108 108
Unit CellA = 200.88 A , B = 200.88 A , C = 200.88 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 1.86 A , Y = 1.86 A , Z = 1.86 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.861.861.86
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z200.880200.880200.880
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS-135-135-135
NC/NR/NS108108108
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.1996.2850.025
Annotation Details3D reconstruction of recombinant DENV-2 sNS1 protein
Supplement
Images
Images

emd_2073.jpg
Sample
NameSecreted form of DENV-2 NS1
Number of Components1
Oligomeric StateHomohexamer
Theoretical Mass0.246 MDa
DetailsMonodisperse sample as assessed by SEC
Component #1: protein - NS1
Scientific nameNon structural protein 1
Common NameNS1
Theoretical Mass0.041 MDa
Oligomeric DetailsHexamer
Number of Copies6
Scientific Name of SpeciesDengue virus 2 (NCBI Taxonomy: 11060)
Common Name of SpeciesDengue virus 2
Recombinant expressionYes
Natural SourceCell Location: Secreted
Engineered SourceVector: pFastBac
Exp System: Spodoptera (NCBI Taxonomy: 7106)
LinksInterPro: IPR:001157
Experiment
Sample Preparation
StainingGrids with adsorbed protein washed with an aqueous solution of 2% (w/v) uranyl acetate for 30 seconds.
Specimen Conc0.1 mg/ml
Specimen Support Details400 mesh copper grid with thin carbon support, glow discharged
Specimen Stateparticle
BufferDetails: 20 mM Tris, 300 mM NaCl
pH: 8
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Date17-SEP-2003
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose60 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 68000 X,
Astigmatismobjective lens astigmatism was corrected at 93,000 times magnification
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus200 nm - 1000 nm
Specimen Holder
HolderFEI single tilt room temperature ( SIDE ENTRY, EUCENTRIC )
Temperature295 Kelvin
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images40
Sampling Size6.35 microns
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmAngular reconstitution
SoftwareIMAGIC, EMAN, XMIPP
DetailsAn exhaustive evaluation of point symmetry was performed as described in the associated manuscript
Resolution By Author23
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages174
Number of Projections3523
DetailsParticles selected semi-automatically using the SWARM-PS software
Download
Data from EMDB
Header (meta data in XML format)emd-2073.xml (7.8 KB)
Map dataemd_2073.map.gz (1.2 MB)
Imagesemd_2073.jpg (37.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2073
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.6 KB