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Structure of immature Dengue virus at low pH

by single particle (icosahedral) reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.691391199, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.691391199, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3c6r, Surface level: 0.691391199, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3c6r, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5006
TitleStructure of immature Dengue virus at low pH
Mapimmature Dengue virus particle at pH 6
Sampleimmature Dengue virus
KeywordsDengue virus, maturation
AuthorsYu I, Zhang W, Holdaway HA, Li L, Kostyuchenko VA, Chipman PR, Kuhn RJ, Rossmann MG, Chen J
DateDeposition: 2008-02-26, Header release: 2008-03-04, Map release: 2009-04-22, Last update: 2011-07-08
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.691391199, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.691391199, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3c6r, Surface level: 0.691391199, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3c6r, Image by Jmol

Supplemental images
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Related Structure Data
Related Entries

PDB-3c6r

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Article
Citation - Primary
ArticleScience, Vol. 319, Issue 5871, Page 1834-7, Year 2008
TitleStructure of the immature dengue virus at low pH primes proteolytic maturation.
AuthorsI-Mei Yu, Wei Zhang, Heather A Holdaway, Long Li, Victor A Kostyuchenko, Paul R Chipman, Richard J Kuhn, Michael G Rossmann, Jue Chen
Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.
KeywordsCryoelectron Microscopy, Crystallography, X-Ray, Dengue Virus (chemistry), Dimerization, E-glycoprotein, Dengue virus type 2, Endoplasmic Reticulum (virology), Furin (metabolism, 3.4.21.75), Hydrogen-Ion Concentration, Image Processing, Computer-Assisted, Membrane Fusion, Protein Conformation, Viral Envelope Proteins (chemistry), Viral Fusion Proteins (chemistry), Viral Matrix Proteins (chemistry), Virion (metabolism), trans-Golgi Network (metabolism)
LinksDOI: 10.1126/science.1153264, PubMed: 18369148
Map
Fileemd_5006.map.gz ( map file in CCP4 format, 64772 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)
255 pix
2.74 A/pix
= 698.7 A
255 pix
2.74 A/pix
= 698.7 A
255 pix
2.74 A/pix
= 698.7 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.15, 0.6913912 (movie #1):
Minimum - Maximum: -2.09156 - 4.29908
Average (Standard dev.): 1.20983e-07 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions255255255
Origin-127-127-127
Limit127127127
Spacing255255255
Unit CellA= B= C: 698.7 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.74 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.742.742.74
M x/y/z255255255
origin x/y/z0.0000.0000.000
length x/y/z698.700698.700698.700
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S213
start NC/NR/NS-127-127-127
NC/NR/NS255255255
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-2.0924.2990.000
Annotation Detailsimmature Dengue virus particle at pH 6
Supplement
Images
Images
Sample
Nameimmature Dengue virus
Number of Components1
Component #1: virus - Dengue
Scientific nameDengue virus
Common NameDengue
Scientific Name of SpeciesDengue virus
Common Name of SpeciesDengue
NCBI taxonomy12637
EmptyNo
EnvelopedYes
IsolateSTRAIN
ClassVIRION
Natural SourceHost Category: VERTEBRATES
Experiment
Sample Preparation
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6
pH: 6
Vitrification
MethodA small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose17 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 51040
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1400 nm - 2900 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature98 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Od Range1
ScannerZEISS SCAI
Number of Digital Images14
Sampling Size7
Quant Bit Number12
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmFourier-Bessel Method
Euler Angles Detailstheta:69-90 degrees phi:(-31)-31 degrees
SoftwareEM3DR
CTF Correctioneach particle
Resolution By Author25 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections231
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
Target CriteriaDensity match
DetailsProtocol: Rigid Body
SoftwareEMfit
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID3c5x
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5006.xml (8.1 KB)
Map dataemd_5006.map.gz (27 MB)
Imagesemd_5006_1.jpg (172.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5006
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, 25.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 25.1 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 440.3 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.6 MB