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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: EMD-1437
TitleSindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
Map dataangel
Sample
  • Sample: Sin-33 Fab treated Sindbis virus
  • Virus: Sindbis virus
  • Protein or peptide: FabFragment antigen-binding
Biological speciesunidentified (others) / Sindbis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsParedes AM / Hernandez R / West M / Brown DT
CitationJournal: J Virol / Year: 2008
Title: Sindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
Authors: Raquel Hernandez / Angel Paredes / Dennis T Brown /
Abstract: A rare Sindbis virus anti-E1 neutralizing monoclonal antibody, Sin-33, was investigated to determine the mechanism of in vitro neutralization. A cryoelectron microscopic reconstruction of Sindbis ...A rare Sindbis virus anti-E1 neutralizing monoclonal antibody, Sin-33, was investigated to determine the mechanism of in vitro neutralization. A cryoelectron microscopic reconstruction of Sindbis virus (SVHR) neutralized with FAb from Sin-33 (FAb-33) revealed conformational changes on the surface of the virion at a resolution of 24 A. FAb-33 was found to bind E1 in less than 1:1 molar ratios, as shown by the absence of FAb density in the reconstruction and stoichiometric measurements using radiolabeled FAb-33, which determined that about 60 molecules of FAb-33 bound to the 240 possible sites in a single virus particle. FAb-33-neutralized virus particles became sensitive to digestion by endoproteinase Glu-C, providing further evidence of antibody-induced structural changes within the virus particle. The treatment of FAb-33-neutralized or Sin-33-neutralized SVHR with low pH did not induce the conformational rearrangements required for virus membrane-cell membrane fusion. Exposure to low pH, however, increased the amount of Sin-33 or FAb-33 that bound to the virus particles, indicating the exposure of additional epitopes. The neutralization of SVHR infection by FAb-33 or Sin-33 did not prevent the association of virus with host cells. These data are in agreement with the results of previous studies that demonstrated that specific antibodies can inactivate the infectious state of a metastable virus in vitro by the induction of conformational changes to produce an inactive structure. A model is proposed which postulates that the induction of conformational changes in the infectious state of a metastable enveloped virus may be a general mechanism of antibody inactivation of virus infectivity.
History
DepositionSep 24, 2007-
Header (metadata) releaseOct 2, 2007-
Map releaseApr 23, 2008-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1437.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationangel
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 256 pix.
= 640. Å
2.5 Å/pix.
x 256 pix.
= 640. Å
2.5 Å/pix.
x 256 pix.
= 640. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density
Contour Level1: 2.31 / Movie #1: 1.2
Minimum - Maximum-6.94307 - 5.38466
Average (Standard dev.)0.00000000057768 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 640 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: Sin-33 Fab treated Sindbis virus
  • Virus: Sindbis virus
  • Protein or peptide: FabFragment antigen-binding

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Supramolecule #1000: Sin-33 Fab treated Sindbis virus

SupramoleculeName: Sin-33 Fab treated Sindbis virus / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 45 MDa / Method: STEM mass measurements Brookhaven, NY.

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Supramolecule #1: Sindbis virus

SupramoleculeName: Sindbis virus / type: virus / ID: 1 / NCBI-ID: 11034 / Sci species name: Sindbis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Culex (mosquito) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Name: Envelope / Diameter: 680 Å / T number (triangulation number): 4
Virus shellShell ID: 2 / Name: Nucleocapsid / Diameter: 400 Å / T number (triangulation number): 4

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Macromolecule #1: Fab

MacromoleculeName: Fab / type: protein_or_peptide / ID: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 20 mM MOPS, 100 mM NaCl
GridDetails: holey carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 110 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: Blot holey carbon grid from behind

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Electron microscopy

MicroscopeJEOL 4000EX
Electron beamAcceleration voltage: 400 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 110 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 60,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 16 µm / Number real images: 6 / Average electron dose: 5 e/Å2

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Image processing

CTF correctionDetails: CTF correction of each particle
Final two d classificationNumber classes: 19
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: MRC
Details: Final map was calculated from 19 class averages using EMAN and imposing icosahedral symmetry
Number images used: 858

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