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Electron cryotomography reveals the portal in the herpesvirus capsid.

by subtomogram averaging

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.12, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.12, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1307
TitleElectron cryotomography reveals the portal in the herpesvirus capsid.
MapThis is the 5-fold-averaged map.
SampleHerpes Simplex Virus 1
AuthorsChang JT, Schmid MF, Rixon FJ, Chiu W
DateDeposition: 2006-11-25, Header release: 2006-12-06, Map release: 2007-12-06, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.12, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.12, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Article
Citation - Primary
ArticleJ. Virol., Vol. 81, Issue 4, Page 2065-8, Year 2007
TitleElectron cryotomography reveals the portal in the herpesvirus capsid.
AuthorsJuan T Chang, Michael F Schmid, Frazer J Rixon, Wah Chiu
KeywordsCapsid (chemistry), Capsid Proteins (isolation & purification), Cryoelectron Microscopy, Electrophoresis, Polyacrylamide Gel, Herpesvirus 1, Human (chemistry), Models, Molecular, Tomography, Urea
LinksDOI: 10.1128/JVI.02053-06, PubMed: 17151101, PMC: PMC1797573
Map
Fileemd_1307.map.gz ( map file in CCP4 format, 93313 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
5.43 A/pix
= 1563.84 A
288 pix
5.43 A/pix
= 1563.84 A
288 pix
5.43 A/pix
= 1563.84 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.119, 0.12 (movie #1):
Minimum - Maximum: -0.232214 - 0.370385
Average (Standard dev.): -0.0147267 (0.0501588)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin-144-144-144
Limit143143143
Spacing288288288
Unit CellA= B= C: 1563.84 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 5.43 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z5.435.435.43
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z1563.8401563.8401563.840
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.2320.370-0.015
Annotation DetailsThis is the 5-fold-averaged map.
Supplement
Images
Images
Sample
NameHerpes Simplex Virus 1
Number of Components1
Component #1: virus - Herpes Simplex
Scientific nameHuman herpesvirus 1
Common NameHerpes Simplex
Scientific Name of SpeciesHuman herpesvirus 1
Common Name of SpeciesHerpes Simplex
NCBI taxonomy10298
EmptyYes
EnvelopedNo
IsolateSPECIES
ClassVIRION
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: INVERTEBRATES
ShellID: 1 , Diameter: 1250 A, Name Element: Capsid , T Number: 16
Experiment
Sample Preparation
Specimen Support Details200 mesh copper grid
BufferDetails: 170mM NaCl, 3.4mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 6.8mM CaCl2, 4.9mM MgCl2
pH: 7.2
Vitrification
Cryogen NameETHANE
Humidity100
Temperature293 Kelvin
InstrumentFEI VITROBOT
DetailsVitrification instrument: Vitrobot
Imaging
MicroscopeJEOL 2010F
DetailsTilted from -70 to +70 in 2 degree increments using Mr T software (unpublished).
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose50 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 20000, Calibrated: 27680
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus3000 nm - 3000 nm
Specimen Holder
HolderSide entry liquid nitrogen cooled
ModelGATAN LIQUID NITROGEN
Tilt Angle70 degrees - 70 degrees
Temperature93 K ( 93 - 93 K)
Camera
DetectorGENERIC GATAN
Processing
Methodsubtomogram averaging
3D reconstruction
AlgorithmWeighted backprojection
SoftwareIMOD
Details5-fold-averaged
Subtomogram Averaging
DetailsAveraged 13 particles extracted from the reconstruction. Average number of tilts used in the 3D reconstructions: 71. Average tomographic tilt angle increment: 2.
Download
Data from EMDB
Header (meta data in XML format)emd-1307.xml (7.1 KB)
Map dataemd_1307.map.gz (52.4 MB)
Images1307.gif (97.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1307
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 20.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 20.3 KB