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- EMDB-9049: Bundibugyo virus glycoprotein in complex with antigen binding fra... -

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Basic information

Entry
Database: EMDB / ID: EMD-9049
TitleBundibugyo virus glycoprotein in complex with antigen binding fragment of chimeric mouse IgG 6D6
Map dataBundibugyo virus glycoprotein in complex with antigen binding fragment of chimeric mouse IgG 6D6
Sample
  • Complex: Bundibugyo virus glycoprotein in complex with antigen binding fragment of chimeric mouse IgG 6D6
    • Complex: Antigen binding fragment of chimeric mouse IgG 6D6
    • Complex: Bundibugyo virus glycoprotein
Biological speciesBundibugyo virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsMilligan JC / Saphire EO
CitationJournal: J Infect Dis / Year: 2019
Title: Structural Characterization of Pan-Ebolavirus Antibody 6D6 Targeting the Fusion Peptide of the Surface Glycoprotein.
Authors: Jacob C Milligan / Diptiben V Parekh / Katherine M Fuller / Manabu Igarashi / Ayato Takada / Erica Ollmann Saphire /
Abstract: Ebola virus infection causes severe disease in humans and represents a global health threat. Candidates for immunotherapeutics and vaccines have shown promise in clinical trials, although they are ...Ebola virus infection causes severe disease in humans and represents a global health threat. Candidates for immunotherapeutics and vaccines have shown promise in clinical trials, although they are ineffective against other members of the Ebolavirus genus that also cause periodic, lethal outbreaks. In this study, we present a crystal structure of a pan-ebolavirus antibody, 6D6, as well as single-particle electron microscopy reconstructions of 6D6 in complex with Ebola and Bundibugyo virus glycoproteins. 6D6 binds to the conserved glycoprotein fusion peptide, implicating it as a site of immune vulnerability that could be exploited to reliably elicit a pan-ebolavirus neutralizing antibody response.
History
DepositionAug 21, 2018-
Header (metadata) releaseAug 29, 2018-
Map releaseSep 26, 2018-
UpdateJan 23, 2019-
Current statusJan 23, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9049.png

Downloads & links

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Map

FileDownload / File: emd_9049.map.gz / Format: CCP4 / Size: 437.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBundibugyo virus glycoprotein in complex with antigen binding fragment of chimeric mouse IgG 6D6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 486 pix.
= 806.76 Å		1.66 Å/pix.
x 486 pix.
= 806.76 Å		1.66 Å/pix.
x 486 pix.
= 806.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-6.3699803 - 20.159672
Average (Standard dev.)-0.013524512 (±0.4865164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions486486486
Spacing486486486
CellA=B=C: 806.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.661.661.66
M x/y/z486486486
origin x/y/z0.0000.0000.000
length x/y/z806.760806.760806.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS486486486
D min/max/mean-6.37020.160-0.014

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Supplemental data

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Sample components

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Entire : Bundibugyo virus glycoprotein in complex with antigen binding fra...

EntireName: Bundibugyo virus glycoprotein in complex with antigen binding fragment of chimeric mouse IgG 6D6
Components
  • Complex: Bundibugyo virus glycoprotein in complex with antigen binding fragment of chimeric mouse IgG 6D6
    • Complex: Antigen binding fragment of chimeric mouse IgG 6D6
    • Complex: Bundibugyo virus glycoprotein

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Supramolecule #1: Bundibugyo virus glycoprotein in complex with antigen binding fra...

SupramoleculeName: Bundibugyo virus glycoprotein in complex with antigen binding fragment of chimeric mouse IgG 6D6
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bundibugyo virus
Recombinant expressionOrganism: Drosophila (fruit flies)
Molecular weightTheoretical: 150 KDa

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Supramolecule #2: Antigen binding fragment of chimeric mouse IgG 6D6

SupramoleculeName: Antigen binding fragment of chimeric mouse IgG 6D6 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Drosophila (fruit flies)

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Supramolecule #3: Bundibugyo virus glycoprotein

SupramoleculeName: Bundibugyo virus glycoprotein / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Bundibugyo virus
Recombinant expressionOrganism: Drosophila (fruit flies)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
25.0 mMTris
100.0 mMNaClSodium chloride
StainingType: NEGATIVE / Material: Uranyl formate
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Details: Negative stain resolution / Number images used: 4182

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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