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6A Electron cryomicroscopy structure of immature Dengue virus serotype 1

by single particle (icosahedral) reconstruction, at 6 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.5, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.5, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4b03, Surface level: 2.5, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-4b03, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2141
Title6A Electron cryomicroscopy structure of immature Dengue virus serotype 1
Mapimmature Dengue virus 1
SampleImmature Dengue virus serotype 1
Keywordsflavivirus, dengue virus serotype 1, immature, e protein, prM protein, capsid protein
AuthorsKostyuchenko VA, Zhang Q, Tan LC, Ng TS, Lok SM
DateDeposition: 2012-06-25, Header release: 2012-07-09, Map release: 2013-06-05, Last update: 2013-06-19
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.5, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.5, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4b03, Surface level: 2.5, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-4b03, Image by Jmol

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

PDB-4b03

CiteFit

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Fit: output model of fitting

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Article
Citation - Primary
ArticleJ. Virol., Vol. 87, Issue 13, Page 7700-7, Year 2013
TitleImmature and mature dengue serotype 1 virus structures provide insight into the maturation process.
AuthorsVictor A Kostyuchenko, Qian Zhang, Joanne L Tan, Thiam-Seng Ng, Shee-Mei Lok
Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore.
KeywordsCryoelectron Microscopy, Dengue Virus (genetics), Models, Molecular, Protein Conformation, Serotyping, Viral Proteins (chemistry)
LinksDOI: 10.1128/JVI.00197-13, PubMed: 23637416, PMC: PMC3700294
Map
Fileemd_2141.map.gz ( map file in CCP4 format, 843751 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.2 A/pix
= 720. A
600 pix
1.2 A/pix
= 720. A
600 pix
1.2 A/pix
= 720. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum: -11.73692226 - 8.14927101
Average (Standard dev.): -0.03639847 (0.68797463)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin-300-300-300
Limit299299299
Spacing600600600
Unit CellA= B= C: 720 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.2 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.21.21.2
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z720.000720.000720.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-11.7378.149-0.036
Annotation Detailsimmature Dengue virus 1
Supplement
Images
Images
Sample
NameImmature Dengue virus serotype 1
Number of Components1
Theoretical Mass14.5MDa
Mass-estimation Methodestimation based on components' amino acid sequences
Experimental Mass14.5MDa
Component #1: virus - Dengue virus 1
Scientific nameDengue virus 1
Theoretical Mass14.5 MDa
Experimental Mass14.5 MDa
Scientific Name of SpeciesDengue virus 1
NCBI taxonomy11053
StrainPVP159 (DEN1/SG/07K3640DK1/2008)
EmptyNo
EnvelopedYes
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 7159
Host Species: Aedes aegypti
Host Category: INVERTEBRATES
ShellID: 1 , Diameter: 600 A, Name Element: E , T Number: 1
Experiment
Sample Preparation
Specimen Support Detailsthin carbon film on lacey carbon support, copper grid, plasma cleaned and glow discharged
Specimen Stateparticle
BufferpH: 7.5
Vitrification
Methodblot 1 second before plunging
Cryogen NameETHANE
Humidity100
InstrumentFEI VITROBOT MARK IV
Temperature100 Kelvin
Imaging
MicroscopeFEI TITAN KRIOS
Date11-APR-2012
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose17.7 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 75000, Calibrated: 75000
AstigmatismAstigmatism was corrected at 250,000 magnification
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Defocus700 nm - 3500 nm
Energy FilterEnergy Filter: FEI
Specimen Holder
ModelFEI TITAN KRIOS AUTOGRID HOLDER
Temperature100 K ( 99 - 101 K)
Camera
DetectorGENERIC GATAN (4k x 4k)
Image Acquisition
#1
Number of Digital Images838
Quant Bit Number16
DetailsCCD data
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmMPSA
SoftwareGPU-adapted, EMAN1
CTF CorrectionWiener filter weighting each particle during 3D reconstruction
Resolution By Author6 A
Resolution MethodFSC 0.143
Single Particle
Number of Projections7169
Detailsparticles were manually selected
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
DetailsProtocol: rigid body. Fit in map feature in Chimera, whole structure was fitted as a rigid body with no apparent need to fit domains separately
SoftwareChimera
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID3c6e
PDB Chain IDA, C
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-2141.xml (8.4 KB)
Map dataemd_2141.map.gz (253.7 MB)
Imagesemd_2141.png (434.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2141
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.7 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 572.3 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.3 MB