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Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.

by single particle (icosahedral) reconstruction, at 9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 75, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 75, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1z8y, Surface level: 100, Image by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-2xfb, Surface level: 100, Image by UCSF CHIMERA

#5: Surface view with fitted model, atomic models: PDB-3muw, Surface level: 100, Image by UCSF CHIMERA

#6: Simplified surface model with fitted atomic model: PDB-1z8y, Image by Jmol

#7: Simplified surface model with fitted atomic model: PDB-2xfb, Image by Jmol

#8: Simplified surface model with fitted atomic model: PDB-3muw, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1121
TitleMapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
Mapcenter of virus is where z=0
SampleSindbis TE12 E2-N318Q
AuthorsMukhopadhyay S, Zhang W, Gabler S, Chipman PR, Strauss EG, Strauss JH, Baker TS, Kuhn RJ, Rossmann MG
DateDeposition: 2005-04-08, Header release: 2005-04-08, Map release: 2006-01-16, Last update: 2013-03-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 75, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 75, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1z8y, Surface level: 100, Image by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-2xfb, Surface level: 100, Image by UCSF CHIMERA

#5: Surface view with fitted model, atomic models: PDB-3muw, Surface level: 100, Image by UCSF CHIMERA

#6: Simplified surface model with fitted atomic model: PDB-1z8y, Image by Jmol

#7: Simplified surface model with fitted atomic model: PDB-2xfb, Image by Jmol

#8: Simplified surface model with fitted atomic model: PDB-3muw, Image by Jmol

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

PDB-1z8y

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Article
Citation - Primary
ArticleStructure, Vol. 14, Issue 1, Page 63-73, Year 2006
TitleMapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
AuthorsSuchetana Mukhopadhyay, Wei Zhang, Stefan Gabler, Paul R Chipman, Ellen G Strauss, James H Strauss, Timothy S Baker, Richard J Kuhn, Michael G Rossmann
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
KeywordsCryoelectron Microscopy, Crystallography, X-Ray, Membrane Glycoproteins (chemistry), Nucleocapsid Proteins (chemistry), Protein Interaction Mapping, Protein Structure, Tertiary, Sindbis Virus (chemistry), Viral Envelope Proteins (chemistry), Viral Fusion Proteins (chemistry), glycoprotein E1, Sindbis virus, glycoprotein E2, Sindbis virus
LinksPII: S0969-2126(05)00393-X, DOI: 10.1016/j.str.2005.07.025, PubMed: 16407066, PMC: PMC2757649
Map
Fileemd_1121.map.gz ( map file in CCP4 format, 335025 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)
441 pix
1.7849886621315 A/pix
= 787.18 A
441 pix
1.7849886621315 A/pix
= 787.18 A
441 pix
1.7849886621315 A/pix
= 787.18 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:138, 75 (movie #1):
Minimum - Maximum: -297.65 - 402.47
Average (Standard dev.): 7.03224 (65.0912)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions441441441
Origin-220-220-220
Limit220220220
Spacing441441441
Unit CellA= B= C: 787.18 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.78499 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.78498866213151.78498866213151.7849886621315
M x/y/z441441441
origin x/y/z0.0000.0000.000
length x/y/z787.180787.180787.180
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ441441441
MAP C/R/S213
start NC/NR/NS-220-220-220
NC/NR/NS441441441
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-297.650402.4707.032
Annotation Detailscenter of virus is where z=0
Supplement
Images
Images
Sample
NameSindbis TE12 E2-N318Q
Number of Components1
DetailsSample is a single deglycosylated virus. For mutagenesis and purification, please see Pletnev et al. (2001) Cell. Virus contains 3 proteins (E1, E2, capsid), a lipid bilyer, and a positive-strand RNA genome.
Component #1: virus - Sindbis strain TE12
Scientific nameSindbis virus
Common NameSindbis strain TE12
Experimental Mass52 MDa
Detailsdeglycosylated virus
Scientific Name of SpeciesSindbis virus
Common Name of SpeciesSindbis strain TE12
NCBI taxonomy11034
EmptyNo
EnvelopedYes
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: INVERTEBRATES
ShellID: 1 , Diameter: 710 A, Name Element: glycoprotein , T Number: 4
ID: 2 , Diameter: 480 A, T Number: 4 , Name Element: lipid bilayer
ID: 3 , T Number: 4 , Diameter: 410 A, Name Element: capsid
Experiment
Sample Preparation
Specimen Conc6 mg/ml
Stainingno staining
Specimen Support Detailsholey carbon 400 mesh copper grid
Specimen Stateparticle
BufferDetails: 20 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA
pH: 7.4
Vitrification
Cryogen NameETHANE
InstrumentHOMEMADE PLUNGER
Methodstandard methods
Time Resolved StateVitrified immediately after blotting.
DetailsVitrification instrument: Purdue manufactured, gravity driven device. Vitrification carried out in hood.
Imaging
MicroscopeFEI/PHILIPS CM200T
Date2000-06-21
DetailsLow dose
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose18 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 38000, Calibrated: 39220
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1100 nm - 2580 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature K ( 87 - 100 K)
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images27
Sampling Size7
Od Range1
Quant Bit Number8
ScannerZEISS SCAI
Detailsoptical density range is 0.33-1.35
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
Algorithmmodel-based common lines
SoftwarePurdue Suite
CTF CorrectionCTF correction of each particle.
Resolution By Author9 A
Resolution MethodFSC 0.5
Euler Angles DetailsEuler angles (theta, phi, omega) are defined as three successive rotations in a right hand coordinate system. First, the viewer is rotated counterclockwise around the z-axis (angle 'phi') and then rotated counterclockwise around the new y-axis (angle 'theta') and rotate clockwise around the new z-axis (angle 'omega').
Detailsresolution determined by splitting data set into two groups.
Single Particle
Number of Projections7085
Number of Class Averages3
DetailsThe particles were selected interactively at the computer terminal.
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid body. each protein in the asymmetric unit was fitting individually.
Refinement Protocolrigid body
Refinement SpaceREAL
Target Criteriasumf
SoftwareEMFIT
PDB Entry ID1I9W
Model #1
Refinement SpaceREAL
Target Criteriasumf
Refinement Protocolrigid body
DetailsProtocol: Rigid body. each protein in the asymmetric unit was fitting individually.
SoftwareEMFIT
PDB Entry ID1XYK
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1121.xml (10.3 KB)
Map dataemd_1121.map.gz (125.3 MB)
Images1121.gif (33.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1121
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.6 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 3.6 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 4.5 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 764.4 KB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.9 MB
movie #7
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.8 MB
movie #8
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.8 MB