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- EMDB-2141: 6A Electron cryomicroscopy structure of immature Dengue virus ser... -

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Basic information

Entry
Database: EMDB / ID: 2141
Title6A Electron cryomicroscopy structure of immature Dengue virus serotype 1
Keywordsflavivirus / dengue virus serotype 1 / immature / e protein / prM protein / capsid protein
SampleImmature Dengue virus serotype 1
SourceDengue virus 1 / virus
Map dataimmature Dengue virus 1
Methodsingle particle (icosahedral) reconstruction, at 6 A resolution
AuthorsKostyuchenko VA / Zhang Q / Tan LC / Ng TS / Lok SM
CitationJ. Virol., 2013, 87, 7700-7707

J. Virol., 2013, 87, 7700-7707 StrPapers
Immature and mature dengue serotype 1 virus structures provide insight into the maturation process.
Victor A Kostyuchenko / Qian Zhang / Joanne L Tan / Thiam-Seng Ng / Shee-Mei Lok

DateDeposition: Jun 25, 2012 / Header (metadata) release: Jul 9, 2012 / Map release: Jun 5, 2013 / Last update: Jun 25, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4b03
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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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.

Voxel sizeX=Y=Z: 1.2 A
Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-11.73692226 - 8.14927101
Average (Standard dev.)-0.03639847 (0.68797463)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin-300-300-300
Limit299299299
Spacing600600600
CellA=B=C: 720 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-11.7378.149-0.036

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Supplemental data

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Sample components

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Entire Immature Dengue virus serotype 1

EntireName: Immature Dengue virus serotype 1 / Number of components: 1
MassTheoretical: 14.5 MDa / Experimental: 14.5 MDa
Measured by: estimation based on components' amino acid sequences

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Component #1: virus, Dengue virus 1

VirusName: Dengue virus 1 / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
MassTheoretical: 14.5 MDa / Experimental: 14.5 MDa
SpeciesSpecies: Dengue virus 1 / virus / Strain: PVP159 (DEN1/SG/07K3640DK1/2008)
Source (natural)Host Species: Aedes aegypti / arthropod / / Host category: INVERTEBRATES
Shell #1Name of element: E / Diameter: 600 A / T number(triangulation number): 1

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
Support filmthin carbon film on lacey carbon support, copper grid, plasma cleaned and glow discharged
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: blot 1 second before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS / Date: Apr 11, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 17.7 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000 X (nominal), 75000 X (calibrated)
Astigmatism: Astigmatism was corrected at 250,000 magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3500 nm / Energy filter: FEI
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 K ( 99 - 101 K)
CameraDetector: GENERIC GATAN (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 838 / Bit depth: 16 / Details: CCD data

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 7169 / Details: particles were manually selected / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: MPSA / Software: GPU-adapted, EMAN1
CTF correction: Wiener filter weighting each particle during 3D reconstruction
Resolution: 6 A / Resolution method: FSC 0.143

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: rigid body. Fit in map feature in Chimera, whole structure was fitted as a rigid body with no apparent need to fit domains separately
Input PDB model: 3c6e
Chain ID: A, C
Output model

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