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- EMDB-6529: Negative stain EM reconstruction of Bundibugyo virus (BDBV) glyco... -

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Entry
Database: EMDB / ID: EMD-6529
TitleNegative stain EM reconstruction of Bundibugyo virus (BDBV) glycoprotein in complex with a human IgG1 Fab
Map dataReconstruction of Fab of human monoclonal antibody BDBV432 in complex with mucin-deleted Bundibugyo virus glycoprotein
Sample
  • Sample: Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibugyo virus in complex with mucin-deleted Bundibugyo virus GP
  • Protein or peptide: human IgG1 monoclonal antibody Fab
  • Protein or peptide: Bundibugyo virus glycoprotein, mucin-deleted
KeywordsEbola virus / EBOV / GP / antibody / Bundibugyo virus / BDBV / Fab
Biological speciesHomo sapiens (human) / Ebola virus sp.
Methodsingle particle reconstruction / Resolution: 17.0 Å
AuthorsFlyak AI / Shen X / Murin CD / Turner HL / Fusco ML / Lampley R / Kose N / Ilinykh PA / Kuzmina N / Branchizio A ...Flyak AI / Shen X / Murin CD / Turner HL / Fusco ML / Lampley R / Kose N / Ilinykh PA / Kuzmina N / Branchizio A / King H / Brown L / Davidson E / Doranz BJ / Slaughter JC / Sapparapu G / Klages C / Ksiazek TG / Saphire EO / Ward AB / Bukreyev A / Crowe JE
CitationJournal: Cell / Year: 2016
Title: Cross-Reactive and Potent Neutralizing Antibody Responses in Human Survivors of Natural Ebolavirus Infection.
Authors: Andrew I Flyak / Xiaoli Shen / Charles D Murin / Hannah L Turner / Joshua A David / Marnie L Fusco / Rebecca Lampley / Nurgun Kose / Philipp A Ilinykh / Natalia Kuzmina / Andre Branchizio / ...Authors: Andrew I Flyak / Xiaoli Shen / Charles D Murin / Hannah L Turner / Joshua A David / Marnie L Fusco / Rebecca Lampley / Nurgun Kose / Philipp A Ilinykh / Natalia Kuzmina / Andre Branchizio / Hannah King / Leland Brown / Christopher Bryan / Edgar Davidson / Benjamin J Doranz / James C Slaughter / Gopal Sapparapu / Curtis Klages / Thomas G Ksiazek / Erica Ollmann Saphire / Andrew B Ward / Alexander Bukreyev / James E Crowe /
Abstract: Recent studies have suggested that antibody-mediated protection against the Ebolaviruses may be achievable, but little is known about whether or not antibodies can confer cross-reactive protection ...Recent studies have suggested that antibody-mediated protection against the Ebolaviruses may be achievable, but little is known about whether or not antibodies can confer cross-reactive protection against viruses belonging to diverse Ebolavirus species, such as Ebola virus (EBOV), Sudan virus (SUDV), and Bundibugyo virus (BDBV). We isolated a large panel of human monoclonal antibodies (mAbs) against BDBV glycoprotein (GP) using peripheral blood B cells from survivors of the 2007 BDBV outbreak in Uganda. We determined that a large proportion of mAbs with potent neutralizing activity against BDBV bind to the glycan cap and recognize diverse epitopes within this major antigenic site. We identified several glycan cap-specific mAbs that neutralized multiple ebolaviruses, including SUDV, and a cross-reactive mAb that completely protected guinea pigs from the lethal challenge with heterologous EBOV. Our results provide a roadmap to develop a single antibody-based treatment effective against multiple Ebolavirus infections.
History
DepositionNov 20, 2015-
Header (metadata) releaseApr 6, 2016-
Map releaseApr 6, 2016-
UpdateApr 6, 2016-
Current statusApr 6, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.85
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.85
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6529.jpg

Downloads & links

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Map

FileDownload / File: emd_6529.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Fab of human monoclonal antibody BDBV432 in complex with mucin-deleted Bundibugyo virus glycoprotein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 80 pix.
= 328. Å		4.1 Å/pix.
x 80 pix.
= 328. Å		4.1 Å/pix.
x 80 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.85 / Movie #1: 4.85
Minimum - Maximum-7.33087778 - 12.607099529999999
Average (Standard dev.)0.0 (±0.99999905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-7.33112.607-0.000

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Supplemental data

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Sample components

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Entire : Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibu...

EntireName: Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibugyo virus in complex with mucin-deleted Bundibugyo virus GP
Components
  • Sample: Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibugyo virus in complex with mucin-deleted Bundibugyo virus GP
  • Protein or peptide: human IgG1 monoclonal antibody Fab
  • Protein or peptide: Bundibugyo virus glycoprotein, mucin-deleted

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Supramolecule #1000: Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibu...

SupramoleculeName: Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibugyo virus in complex with mucin-deleted Bundibugyo virus GP
type: sample / ID: 1000
Oligomeric state: Three Fabs (each consisting of one heavy chain and one light chain) bind to a single GP (consisting of a trimer of heterodimers of GP1 and GP2)
Number unique components: 2
Molecular weightTheoretical: 310 KDa

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Macromolecule #1: human IgG1 monoclonal antibody Fab

MacromoleculeName: human IgG1 monoclonal antibody Fab / type: protein_or_peptide / ID: 1 / Name.synonym: Fab
Details: Fabs were generated by optimized papain proteolysis of IgG1. There are three Fabs bound to each trimeric GP.
Number of copies: 3
Oligomeric state: heterodimer (one heavy chain, one light chain)
Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: Peripheral blood mononuclear cells
Molecular weightTheoretical: 50 KDa

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Macromolecule #2: Bundibugyo virus glycoprotein, mucin-deleted

MacromoleculeName: Bundibugyo virus glycoprotein, mucin-deleted / type: protein_or_peptide / ID: 2 / Name.synonym: BDBV GPdMuc
Details: Recombinantly expressed ectodomain of Bundibugyo virus GP. Mucin-like domains were deleted from the expression construct, as were the transmembrane domains and cytoplasmic tail.
Number of copies: 1
Oligomeric state: trimer of heterodimers (consisting of covalently linked GP1 and GP2)
Recombinant expression: Yes
Source (natural)Organism: Ebola virus sp. / Strain: Bundibugyo virus
Molecular weightTheoretical: 160 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly) / Recombinant cell: S2 / Recombinant plasmid: pMT puro

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris, 150 mM NaCl
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
DateMar 5, 2015
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 73
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 12008

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