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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: EMD-1661
TitleThe three-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy
Map dataTop view of the EM density map of the HCV p7 channel
Sample
  • Sample: HCV p7 hexamer, JFH-1 strain, genotype 2a
  • Protein or peptide: p7
Biological speciesHepatitis C virus
Methodsingle particle reconstruction / negative staining / Resolution: 16.0 Å
AuthorsLuik P / Chew C / Aittoniemi J / Chang J / Wentworth P / Dwek RA / Biggin PC / Venien-Bryan C / Zitzmann N
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: The 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy.
Authors: Philipp Luik / Chee Chew / Jussi Aittoniemi / Jason Chang / Paul Wentworth / Raymond A Dwek / Philip C Biggin / Catherine Vénien-Bryan / Nicole Zitzmann /
Abstract: Infection with the hepatitis C virus (HCV) has a huge impact on global health putting more than 170 million people at risk of developing severe liver disease. The HCV encoded p7 ion channel is ...Infection with the hepatitis C virus (HCV) has a huge impact on global health putting more than 170 million people at risk of developing severe liver disease. The HCV encoded p7 ion channel is essential for the production of infectious viruses. Despite a growing body of functional data, little is known about the 3-dimensional (3D) structure of the channel. Here, we present the 3D structure of a full-length viroporin, the detergent-solubilized hexameric 42 kDa form of the HCV p7 ion channel, as determined by single-particle electron microscopy using the random conical tilting approach. The reconstruction of such a small protein complex was made possible by a combination of high-contrast staining, the symmetry, and the distinct structural features of the channel. The orientation of the p7 monomers within the density was established using immunolabeling with N and C termini specific F(ab) fragments. The density map at a resolution of approximately 16 A reveals a flower-shaped protein architecture with protruding petals oriented toward the ER lumen. This broadest part of the channel presents a comparatively large surface area providing potential interaction sites for cellular and virally encoded ER resident proteins.
History
DepositionNov 4, 2009-
Header (metadata) releaseNov 17, 2009-
Map releaseNov 17, 2009-
UpdateNov 17, 2009-
Current statusNov 17, 2009Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_1661.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTop view of the EM density map of the HCV p7 channel
Voxel sizeX=Y=Z: 2.77 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.0164729 - 0.0843588
Average (Standard dev.)0.00149795 (±0.00843059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 177.28 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: HCV p7 hexamer, JFH-1 strain, genotype 2a
  • Protein or peptide: p7

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Supramolecule #1000: HCV p7 hexamer, JFH-1 strain, genotype 2a

SupramoleculeName: HCV p7 hexamer, JFH-1 strain, genotype 2a / type: sample / ID: 1000 / Oligomeric state: Hexameric / Number unique components: 1

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Macromolecule #1: p7

MacromoleculeName: p7 / type: protein_or_peptide / ID: 1 / Name.synonym: p7 / Details: p7 solubilzed with DHPC / Recombinant expression: No
Source (natural)Organism: Hepatitis C virus

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Details: 100 mM NaCl, 50 mM DHPC, 25 mM Hepes, pH 7.0
StainingType: NEGATIVE / Details: 2% (w/v) phosphotungstic acid (PTA)
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Eucentric / Specimen holder model: PHILIPS ROTATION HOLDER
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF

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