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- EMDB-2655: Electron Cryo-microscopy of Venezuelan Equine Encephalitis Virus ... -

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Entry
Database: EMDB / ID: EMD-2655
TitleElectron Cryo-microscopy of Venezuelan Equine Encephalitis Virus TC-83 in complex with neutralizing antibody Fab 3B4C-4
Map dataReconstruction of VEEV TC-83 in complex with a Fab fragment from neutralizing antibody 3B4C-4.
Sample
  • Sample: VEEV TC-83 in complex with Fab fragments of neutralizing antibody 3B4C-4.
  • Virus: Venezuelan equine encephalitis virus (strain TC-83)
  • Protein or peptide: Fab fragments of neutralizing antibody 3B4C-4
KeywordsAlphavirus / Venezuelan / antibody neutralization / Fab
Biological speciesMus musculus (house mouse) / Venezuelan equine encephalitis virus (strain TC-83)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsPorta JC / Jose J / Roehrig JT / Blair CD / Kuhn RJ / Rossmann MG
CitationJournal: J Virol / Year: 2014
Title: Locking and blocking the viral landscape of an alphavirus with neutralizing antibodies.
Authors: Jason Porta / Joyce Jose / John T Roehrig / Carol D Blair / Richard J Kuhn / Michael G Rossmann /
Abstract: Alphaviruses are serious, sometimes lethal human pathogens that belong to the family Togaviridae. The structures of human Venezuelan equine encephalitis virus (VEEV), an alphavirus, in complex with ...Alphaviruses are serious, sometimes lethal human pathogens that belong to the family Togaviridae. The structures of human Venezuelan equine encephalitis virus (VEEV), an alphavirus, in complex with two strongly neutralizing antibody Fab fragments (F5 and 3B4C-4) have been determined using a combination of cryo-electron microscopy and homology modeling. We characterize these monoclonal antibody Fab fragments, which are known to abrogate VEEV infectivity by binding to the E2 (envelope) surface glycoprotein. Both of these antibody Fab fragments cross-link the surface E2 glycoproteins and therefore probably inhibit infectivity by blocking the conformational changes that are required for making the virus fusogenic. The F5 Fab fragment cross-links E2 proteins within one trimeric spike, whereas the 3B4C-4 Fab fragment cross-links E2 proteins from neighboring spikes. Furthermore, F5 probably blocks the receptor-binding site, whereas 3B4C-4 sterically hinders the exposure of the fusion loop at the end of the E2 B-domain.
IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Venezuelan equine encephalitis virus (VEEV) is an alphavirus with a wide distribution across the globe. No effective vaccines ...IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Venezuelan equine encephalitis virus (VEEV) is an alphavirus with a wide distribution across the globe. No effective vaccines exist for alphaviral infections. Therefore, a better understanding of VEEV and its associated neutralizing antibodies will help with the development of effective drugs and vaccines.
History
DepositionMay 18, 2014-
Header (metadata) releaseJun 18, 2014-
Map releaseJun 25, 2014-
UpdateOct 1, 2014-
Current statusOct 1, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-4uok
  • Surface level: 1
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4uok
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Structure viewerEM map:
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Supplemental images

EMD-2655.png

Downloads & links

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Map

FileDownload / File: emd_2655.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of VEEV TC-83 in complex with a Fab fragment from neutralizing antibody 3B4C-4.
Voxel sizeX=Y=Z: 4.28 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.62350607 - 4.36190176
Average (Standard dev.)-0.00027812 (±0.48838764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 1095.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.284.284.28
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z1095.6801095.6801095.680
α/β/γ90.00090.00090.000
start NX/NY/NZ0-51-100
NX/NY/NZ82103201
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-4.6244.362-0.000

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Supplemental data

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Sample components

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Entire : VEEV TC-83 in complex with Fab fragments of neutralizing antibody...

EntireName: VEEV TC-83 in complex with Fab fragments of neutralizing antibody 3B4C-4.
Components
  • Sample: VEEV TC-83 in complex with Fab fragments of neutralizing antibody 3B4C-4.
  • Virus: Venezuelan equine encephalitis virus (strain TC-83)
  • Protein or peptide: Fab fragments of neutralizing antibody 3B4C-4

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Supramolecule #1000: VEEV TC-83 in complex with Fab fragments of neutralizing antibody...

SupramoleculeName: VEEV TC-83 in complex with Fab fragments of neutralizing antibody 3B4C-4.
type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 5.25 MDa / Theoretical: 5.25 MDa / Method: UV-VIS

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Supramolecule #1: Venezuelan equine encephalitis virus (strain TC-83)

SupramoleculeName: Venezuelan equine encephalitis virus (strain TC-83) / type: virus / ID: 1 / Name.synonym: VEEV / NCBI-ID: 11037
Sci species name: Venezuelan equine encephalitis virus (strain TC-83)
Sci species strain: TC-83 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: VEEV
Host (natural)Organism: Equus asinus (ass) / synonym: VERTEBRATES
Host systemRecombinant cell: BHK-15
Molecular weightExperimental: 5.25 MDa / Theoretical: 5.25 MDa
Virus shellShell ID: 1 / Name: E1E2 / Diameter: 700 Å / T number (triangulation number): 4

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Macromolecule #1: Fab fragments of neutralizing antibody 3B4C-4

MacromoleculeName: Fab fragments of neutralizing antibody 3B4C-4 / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Mus musculus (house mouse)

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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

Concentration1.0 mg/mL
BufferpH: 7.6 / Details: 50 mM TRIS-HCl, 100 mM NaCl, 0.1 M EDTA
GridDetails: 200 mesh Cu Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 130 K / Instrument: HOMEMADE PLUNGER / Details: Grids prepared under BSL-2 hood / Method: Blot for 5 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60521 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Specialist opticsEnergy filter - Name: FEI / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 50.0 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 100 K / Max: 105 K / Average: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 96,000 times magnification
DateOct 14, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 104 / Average electron dose: 24 e/Å2 / Od range: 1.5 / Bits/pixel: 8
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle/image
Final two d classificationNumber classes: 10
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: OTHER / Software - Name: EMAN1/2 / Number images used: 1120
DetailsThe particles were selected manually using the EMAN2 boxing program.

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