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The three-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy

by single particle reconstruction, at 16 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.035, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.035, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1661
TitleThe three-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy
MapTop view of the EM density map of the HCV p7 channel
SampleHCV p7 hexamer, JFH-1 strain, genotype 2a
AuthorsLuik P, Chew C, Aittoniemi J, Chang J, Wentworth P, Dwek RA, Biggin PC, Venien-Bryan C, Zitzmann N
DateDeposition: 2009-11-04, Header release: 2009-11-17, Map release: 2009-11-17, Last update: 2009-11-17
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.035, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.035, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 106, Issue 31, Page 12712-6, Year 2009
TitleThe 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy.
AuthorsPhilipp Luik, Chee Chew, Jussi Aittoniemi, Jason Chang, Paul Wentworth, Raymond A Dwek, Philip C Biggin, Catherine Vénien-Bryan, Nicole Zitzmann
Department of Biochemistry and Oxford Glycobiology Institute, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
KeywordsImaging, Three-Dimensional, Microscopy, Electron, Microscopy, Immunoelectron, Models, Molecular, Viral Proteins (chemistry), p7 protein, Hepatitis C virus
LinksDOI: 10.1073/pnas.0905966106, PubMed: 19590017, PMC: PMC2722341
Map
Fileemd_1661.map.gz ( map file in CCP4 format, 1025 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum: -0.0164729 - 0.0843588
Average (Standard dev.): 0.00149795 (0.00843059)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-32-32
Limit313131
Spacing646464
Unit CellA= B= C: 177.28 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.77 A
CCP4 map header info
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/NZ000
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0160.0840.001
Annotation DetailsTop view of the EM density map of the HCV p7 channel
Supplement
Images
Images
Sample
NameHCV p7 hexamer, JFH-1 strain, genotype 2a
Number of Components1
Oligomeric StateHexameric
Component #1: protein - p7
Scientific namep7
Detailsp7 solubilzed with DHPC
Scientific Name of SpeciesHepatitis C virus
NCBI taxonomy11103
Recombinant expressionNo
Experiment
Sample Preparation
Staining2% (w/v) phosphotungstic acid (PTA)
Specimen Stateparticle
BufferDetails: 100 mM NaCl, 50 mM DHPC, 25 mM Hepes, pH 7.0
pH: 7
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI/PHILIPS CM120T
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Illumination ModeSPOT SCAN
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderEucentric
ModelPHILIPS ROTATION HOLDER
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerNIKON SUPER COOLSCAN 9000
Processing
Methodsingle particle reconstruction
3D reconstruction
Resolution By Author16 A
Resolution MethodFSC 0.5
Single Particle
Applied SymmetryC6 (6 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-1661.xml (5.7 KB)
Map dataemd_1661.map.gz (968.9 KB)
ImagesPreview_EMD-1661.tif (256.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1661
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 26.4 KB