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Sindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.

by single particle (icosahedral) reconstruction, at 24 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.2, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.2, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1437
TitleSindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
Mapangel
SampleSin-33 Fab treated Sindbis virus
AuthorsParedes AM, Hernandez R, West M, Brown DT
DateDeposition: 2007-09-24, Header release: 2007-10-02, Map release: 2008-04-23, 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: 1.2, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.2, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Virol., Vol. 82, Issue 12, Page 5750-60, Year 2008
TitleSindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
AuthorsRaquel Hernandez, Angel Paredes, Dennis T Brown
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27608, USA.
KeywordsAnimals, Antibodies, Monoclonal (pharmacology), Cricetinae, Epitopes, Hydrogen-Ion Concentration, Immunoglobulin Fab Fragments (immunology), Kidney (cytology), Membrane Glycoproteins (immunology), Neutralization Tests, Peptide Mapping, Protein Binding, Protein Conformation, Sindbis Virus (chemistry), Viral Envelope Proteins (immunology), Virion (physiology), glycoprotein E1, Sindbis virus
LinksDOI: 10.1128/JVI.02673-07, PubMed: 18417595, PMC: PMC2395122
Map
Fileemd_1437.map.gz ( map file in CCP4 format, 65537 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
2.5 A/pix
= 640. A
256 pix
2.5 A/pix
= 640. A
256 pix
2.5 A/pix
= 640. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2.31, 1.2 (movie #1):
Minimum - Maximum: -6.94307 - 5.38466
Average (Standard dev.): 5.7768e-10 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
Unit CellA= B= C: 640 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.5 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.52.52.5
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z640.000640.000640.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-6.9435.3850.000
Annotation Detailsangel
Supplement
Images
Images
Sample
NameSin-33 Fab treated Sindbis virus
Number of Components2
Theoretical Mass45MDa
Mass-estimation MethodSTEM mass measurements Brookhaven, NY.
Component #1: protein - Fab
Scientific nameFab
Oligomeric Detailsmonomer
Scientific Name of Speciesunidentified
NCBI taxonomy32644
Recombinant expressionYes
Component #2: virus - Sindbis virus
Scientific nameSindbis virus
Scientific Name of SpeciesSindbis virus
NCBI taxonomy11034
IsolateSTRAIN
EmptyNo
ClassVIRION
EnvelopedYes
Natural SourceNCBI taxonomy: 53527
Host Species: Culex
Host Category: INVERTEBRATES
ShellID: 1 , Name Element: Envelope , Diameter: 680 A, T Number: 4
ID: 2 , Name Element: Nucleocapsid , T Number: 4 , Diameter: 400 A
Experiment
Sample Preparation
Specimen Support Detailsholey carbon film
Specimen Stateparticle
BufferDetails: 20 mM MOPS, 100 mM NaCl
pH: 7.4
Vitrification
Cryogen NameETHANE
Temperature110 Kelvin
InstrumentHOMEMADE PLUNGER
MethodBlot holey carbon grid from behind
DetailsVitrification instrument: plunger
Imaging
MicroscopeJEOL 4000EX
Electron Gun
Electron SourceLAB6
Accelerating Voltage400 kV
Electron Dose5 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Astigmatismobjective lens astigmatism was corrected at 60,000 times magnification
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 3000 nm
Specimen Holder
HolderSide entry liquid nitrogen cooled
ModelGATAN LIQUID NITROGEN
Temperature110 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images6
Sampling Size16
ScannerZEISS SCAI
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
SoftwareMRC
CTF CorrectionCTF correction of each particle
Resolution By Author24 A
Resolution MethodFSC
DetailsFinal map was calculated from 19 class averages using EMAN and imposing icosahedral symmetry
Single Particle
Number of Projections858
Number of Class Averages19
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-1437.xml (7.8 KB)
Map dataemd_1437.map.gz (21 MB)
Images1437.gif (95.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1437
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.6 MB
Session file for UCSF-Chimera, 26.8 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, 26.8 KB