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The first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike.

by single particle (icosahedral) reconstruction, at 9.0 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 961, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 961, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1018
TitleThe first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike.
MapSemliki forest virus
SampleSemliki forest mSQL
AuthorsFuller SD
DateDeposition: 2002-12-12, Header release: 2003-01-06, Map release: 2003-01-06, Last update: 2012-10-17
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 961, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 961, Made by UCSF CHIMERA

Supplemental images

1018.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

PDB-3izl

EMDB-1963

PDB-3j03

EMDB-5154

EMDB-5248
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 283, Issue 1, Page 71-81, Year 1998
TitleThe first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike.
AuthorsI Ferlenghi, B Gowen, F de Haas, E J Mancini, H Garoff, M Sjöberg, S D Fuller
Structural Biology Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
KeywordsImage Processing, Computer-Assisted, Microscopy, Electron (methods), Protein Conformation, Protein Precursors (chemistry), Semliki forest virus (ultrastructure), Viral Envelope Proteins (chemistry), Virion (ultrastructure)
LinksPubMed: 9761674, PII: S0022-2836(98)92066-6, DOI: 10.1006/jmbi.1998.2066
Map
FileEMD-1018.map ( map file in CCP4 format, 33555.456 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:992, 961 (movie #1):
Minimum - Maximum: -6796 - 3204
Average (Standard dev.): 7.4848 (394.451)
Data Typeinteger (16-bit)
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
Unit CellA= B= C: 256 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1 A
CCP4 map header info
modeImage stored as Integer*27
A/pix X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-6796.0003204.0007.485
Annotation DetailsSemliki forest virus
Supplement
Images
Images

1018.gif
Sample
NameSemliki forest mSQL
Number of Components1
Component #1: virus - semliki forest m SQL
Scientific nameSemliki forest virus
Common Namesemliki forest m SQL
DetailsmSQL mutation.
Scientific Name of SpeciesSemliki forest virus
Common Name of Speciessemliki forest m SQL
NCBI taxonomy11033
EmptyNo
EnvelopedYes
IsolateSTRAIN
ClassVIRION
Natural SourceHost Species: baby hamster kidney 21 cells
Host Category: VERTEBRATES
ShellId: 1 , Name Element: envelope , T Number: 4
Id: 2 , T Number: 4 , Name Element: nucleo capsid
Experiment
Sample Preparation
Specimen Conc3 mg/ml
Specimen Stateparticle
BufferDetails: tris(10mM) NaCL (100mM) ph 7.4
pH: 7.4
Vitrification
Cryogen NameETHANE
Humidity100
Temperature37 Kelvin
InstrumentHOMEMADE PLUNGER
Methodblot for 2 sec Graticule grids were used to maintain
DetailsVitrification instrument: EMBL plunger with warm humid air spray
Imaging
MicroscopeFEI/PHILIPS CM200FEG/ST
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose8 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus975 nm - 7628 nm
Specimen Holder
Holdereucentric
ModelGATAN LIQUID NITROGEN
Temperature105 K
Camera
DetectorSO163 film
Distance44
Image Acquisition
Sampling Size20
Od Range1
Quant Bit Number8
ScannerPERKIN ELMER
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
Algorithmfourier bessel
SoftwareEMBL
CTF Correctionctf multiplication and summation of normalized reconstructions
Resolution By Author9 A
Resolution MethodFSC at 0.5 cut off
Euler Angles Detailssufficient to give maximum inverse eigen value of 0.1
Single Particle
Number of Projections62
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-1018.xml (7.4 KB)
Map dataemd_1018.map.gz (21.7 MB)
Images1018.gif (45.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1018
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, 19.7 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, 19.7 KB