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- EMDB-1437: Sindbis virus conformational changes induced by a neutralizing an... -

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Basic information

Entry
Database: EMDB / ID: 1437
TitleSindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
SampleSin-33 Fab treated Sindbis virus
SourceUnidentified
Sindbis virus / virus / シンドビスウイルス
Map dataangel
Methodsingle particle (icosahedral) reconstruction, at 24 A resolution
AuthorsParedes AM / Hernandez R / West M / Brown DT
CitationJ. Virol., 2008, 82, 5750-5760

J. Virol., 2008, 82, 5750-5760 StrPapers
Sindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
Raquel Hernandez / Angel Paredes / Dennis T Brown

DateDeposition: Sep 24, 2007 / Header (metadata) release: Oct 2, 2007 / Map release: Apr 23, 2008 / Last update: Sep 24, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_1437.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices
Size
Brightness
Contrast
Others
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.

Voxel sizeX=Y=Z: 2.5 A
Density
Contour Level:2.31, 1.2 (movie #1):
Minimum - Maximum-6.94307 - 5.38466
Average (Standard dev.)5.7768e-10 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 640 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-6.9435.3850.000

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Supplemental data

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Sample components

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Entire Sin-33 Fab treated Sindbis virus

EntireName: Sin-33 Fab treated Sindbis virus / Number of components: 2
MassTheoretical: 45 MDa / Measured by: STEM mass measurements Brookhaven, NY.

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Component #1: protein, Fab

ProteinName: Fab / Oligomeric Details: monomer / Recombinant expression: Yes
SourceSpecies: Unidentified

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Component #2: virus, Sindbis virus

VirusName: Sindbis virus / Class: VIRION / Isolate: STRAIN / Empty: No / Enveloped: Yes
SpeciesSpecies: Sindbis virus / virus / シンドビスウイルス
Source (natural)Host Species: Culex / arthropod / Host category: INVERTEBRATES
Shell #1Name of element: Envelope / Diameter: 680 A / T number(triangulation number): 4
Shell #2Name of element: Nucleocapsid / Diameter: 400 A / T number(triangulation number): 4

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 20 mM MOPS, 100 mM NaCl / pH: 7.4
Support filmholey carbon film
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 110 K / Method: Blot holey carbon grid from behind / Details: Vitrification instrument: plunger

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Electron microscopy imaging

ImagingMicroscope: JEOL 4000EX
Electron gunElectron source: LAB6 / Accelerating voltage: 400 kV / Electron dose: 5 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal)
Astigmatism: objective lens astigmatism was corrected at 60,000 times magnification
Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
Specimen HolderHolder: Side entry liquid nitrogen cooled / Model: GATAN LIQUID NITROGEN / Temperature: 110 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 6 / Scanner: ZEISS SCAI / Sampling size: 16 microns

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 858 / Number of class averages: 19 / Applied symmetry: I (icosahedral)
3D reconstructionSoftware: MRC / CTF correction: CTF correction of each particle / Resolution: 24 A / Resolution method: FSC
Details: Final map was calculated from 19 class averages using EMAN and imposing icosahedral symmetry

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