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- EMDB-1661: The three-dimensional structure of a hepatitis C virus p7 ion cha... -

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Basic information

Entry
Database: EMDB / ID: 1661
TitleThe three-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy
SampleHCV p7 hexamer, JFH-1 strain, genotype 2a
SourceHepatitis C virus / virus
Map dataTop view of the EM density map of the HCV p7 channel
Methodsingle particle reconstruction, at 16 A resolution
AuthorsLuik P / Chew C / Aittoniemi J / Chang J / Wentworth P / Dwek RA / Biggin PC / Venien-Bryan C / Zitzmann N
CitationProc. Natl. Acad. Sci. U.S.A., 2009, 106, 12712-12716

Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 12712-12716 StrPapers
The 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy.
Philipp Luik / Chee Chew / Jussi Aittoniemi / Jason Chang / Paul Wentworth / Raymond A Dwek / Philip C Biggin / Catherine Vénien-Bryan / Nicole Zitzmann

DateDeposition: Nov 4, 2009 / Header (metadata) release: Nov 17, 2009 / Map release: Nov 17, 2009 / Last update: Nov 4, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1661.map.gz (map file in CCP4 format, 1025 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
2.77 A/pix
= 177.28 A
64 pix
2.77 A/pix
= 177.28 A
64 pix
2.77 A/pix
= 177.28 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.77 A
Density
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.0164729 - 0.0843588
Average (Standard dev.)0.00149795 (0.00843059)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-32-32
Limit313131
Spacing646464
CellA=B=C: 177.28 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.772.772.77
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z177.280177.280177.280
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-147-147-147
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-0.0160.0840.001

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Supplemental data

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Sample components

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Entire HCV p7 hexamer, JFH-1 strain, genotype 2a

EntireName: HCV p7 hexamer, JFH-1 strain, genotype 2a / Number of components: 1 / Oligomeric State: Hexameric

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Component #1: protein, p7

ProteinName: p7 / a.k.a: p7 / Details: p7 solubilzed with DHPC / Recombinant expression: No
SourceSpecies: Hepatitis C virus / virus

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 100 mM NaCl, 50 mM DHPC, 25 mM Hepes, pH 7.0
pH: 7
Staining2% (w/v) phosphotungstic acid (PTA)
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM120T
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: PHILIPS ROTATION HOLDER
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: NIKON SUPER COOLSCAN 9000

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 16 A / Resolution method: FSC 0.5

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