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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, Made by UCSF CHIMERA

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

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
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
Graduate Program in Structural and Computational Biology and Molecular Biophysics, National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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