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- EMDB-5006: Structure of immature Dengue virus at low pH -

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Basic information

Entry
Database: EMDB / ID: 5006
TitleStructure of immature Dengue virus at low pH
KeywordsDengue virus / maturation
Sampleimmature Dengue virus
SourceDengue virus / virus / Dengue / デングウイルス
Map dataimmature Dengue virus particle at pH 6
Methodsingle particle (icosahedral) reconstruction, at 25 A resolution
AuthorsYu I / Zhang W / Holdaway HA / Li L / Kostyuchenko VA / Chipman PR / Kuhn RJ / Rossmann MG / Chen J
CitationScience, 2008, 319, 1834-1837

Science, 2008, 319, 1834-1837 StrPapers
Structure of the immature dengue virus at low pH primes proteolytic maturation.
I-Mei Yu / Wei Zhang / Heather A Holdaway / Long Li / Victor A Kostyuchenko / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / Jue Chen

DateDeposition: Feb 26, 2008 / Header (metadata) release: Mar 4, 2008 / Map release: Apr 22, 2009 / Last update: Feb 26, 2008

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.691391199
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.691391199
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3c6r
  • Surface level: 0.691391199
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5006.map.gz (map file in CCP4 format, 64772 KB)
Projections & slices
Size
Brightness
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Others
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.

Voxel sizeX=Y=Z: 2.74 A
Density
Contour Level:1.15, 0.6913912 (movie #1):
Minimum - Maximum-2.09156 - 4.29908
Average (Standard dev.)1.20983e-07 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions255255255
Origin-127-127-127
Limit127127127
Spacing255255255
CellA=B=C: 698.7 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-2.0924.2990.000

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Supplemental data

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Sample components

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Entire immature Dengue virus

EntireName: immature Dengue virus / Number of components: 1

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Component #1: virus, Dengue virus

VirusName: Dengue virus / a.k.a: Dengue / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Dengue virus / virus / Dengue / デングウイルス
Source (natural)Host category: VERTEBRATES

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 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
Support film400 mesh copper grid
VitrificationInstrument: NONE / Cryogen name: ETHANE
Method: A 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.

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 51040 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 2900 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 14 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 231 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Fourier-Bessel Method / Euler angles: theta:69-90 degrees phi:(-31)-31 degrees / Software: EM3DR / CTF correction: each particle / Resolution: 25 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: EMfit / Refinement protocol: rigid body / Target criteria: Density match / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 3c5x
Output model

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