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

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Basic information

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 Å 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 Yorodumi Papers
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

Validation ReportPDB-ID: 3c6r

SummaryFull reportAbout validation report
DateDeposition: Feb 26, 2008 / Header (metadata) release: Mar 4, 2008 / Map release: Apr 22, 2009 / Last update: Jul 8, 2011

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.691391199
  • Imaged by UCSF CHIMERA
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  • 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
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3c6r
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


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

Image control

AxesZ (Sec.)X (Row.)Y (Col.)
255 pix
2.74 Å/pix.
= 698.7 Å
255 pix
2.74 Å/pix.
= 698.7 Å
255 pix
2.74 Å/pix.
= 698.7 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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


Space Group Number1
Map Geometry
Axis orderYXZ
CellA=B=C: 698.7 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
start NX/NY/NZ-127-127-127
MAP C/R/S213
start NC/NR/NS-127-127-127
D min/max/mean-2.0924.2990.000

Supplemental data

Sample components

Entire immature Dengue virus

EntireName: immature Dengue virus / Number of components: 1

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

Experimental details

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.

Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/Å2 / 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

Image acquisition

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

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 Å / Resolution method: FSC 0.5

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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