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- EMDB-8701: EBOV GPdMuc:ADI-15946 -

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Basic information

Entry
Database: EMDB / ID: EMD-8701
TitleEBOV GPdMuc:ADI-15946
Map dataComplex of recombinant Ebola virus glycoprotein with human IgG1 Fab ADI-15946 from survivor.
Sample
  • Complex: EBOV GPdMuc:ADI-15946
    • Complex: EBOV GPdMuc
    • Complex: ADI-15946 Fab
    • Complex: ADI-15946 Fab
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 24.7 Å
AuthorsMurin CD / Ward AB / Turner HL
CitationJournal: Cell / Year: 2017
Title: Antibodies from a Human Survivor Define Sites of Vulnerability for Broad Protection against Ebolaviruses.
Authors: Anna Z Wec / Andrew S Herbert / Charles D Murin / Elisabeth K Nyakatura / Dafna M Abelson / J Maximilian Fels / Shihua He / Rebekah M James / Marc-Antoine de La Vega / Wenjun Zhu / Russell R ...Authors: Anna Z Wec / Andrew S Herbert / Charles D Murin / Elisabeth K Nyakatura / Dafna M Abelson / J Maximilian Fels / Shihua He / Rebekah M James / Marc-Antoine de La Vega / Wenjun Zhu / Russell R Bakken / Eileen Goodwin / Hannah L Turner / Rohit K Jangra / Larry Zeitlin / Xiangguo Qiu / Jonathan R Lai / Laura M Walker / Andrew B Ward / John M Dye / Kartik Chandran / Zachary A Bornholdt /
Abstract: Experimental monoclonal antibody (mAb) therapies have shown promise for treatment of lethal Ebola virus (EBOV) infections, but their species-specific recognition of the viral glycoprotein (GP) has ...Experimental monoclonal antibody (mAb) therapies have shown promise for treatment of lethal Ebola virus (EBOV) infections, but their species-specific recognition of the viral glycoprotein (GP) has limited their use against other divergent ebolaviruses associated with human disease. Here, we mined the human immune response to natural EBOV infection and identified mAbs with exceptionally potent pan-ebolavirus neutralizing activity and protective efficacy against three virulent ebolaviruses. These mAbs recognize an inter-protomer epitope in the GP fusion loop, a critical and conserved element of the viral membrane fusion machinery, and neutralize viral entry by targeting a proteolytically primed, fusion-competent GP intermediate (GP) generated in host cell endosomes. Only a few somatic hypermutations are required for broad antiviral activity, and germline-approximating variants display enhanced GP recognition, suggesting that such antibodies could be elicited more efficiently with suitably optimized GP immunogens. Our findings inform the development of both broadly effective immunotherapeutics and vaccines against filoviruses.
History
DepositionApr 21, 2017-
Header (metadata) releaseJun 7, 2017-
Map releaseJun 7, 2017-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.62
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.62
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8701.png

Downloads & links

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Map

FileDownload / File: emd_8701.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex of recombinant Ebola virus glycoprotein with human IgG1 Fab ADI-15946 from survivor.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 64 pix.
= 262.4 Å		4.1 Å/pix.
x 64 pix.
= 262.4 Å		4.1 Å/pix.
x 64 pix.
= 262.4 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: 3.62 / Movie #1: 3.62
Minimum - Maximum-3.8835473 - 11.143057000000001
Average (Standard dev.)0.01960954 (±0.98014253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-3.88411.1430.020

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Supplemental data

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Sample components

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Entire : EBOV GPdMuc:ADI-15946

EntireName: EBOV GPdMuc:ADI-15946
Components
  • Complex: EBOV GPdMuc:ADI-15946
    • Complex: EBOV GPdMuc
    • Complex: ADI-15946 Fab
    • Complex: ADI-15946 Fab

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Supramolecule #1: EBOV GPdMuc:ADI-15946

SupramoleculeName: EBOV GPdMuc:ADI-15946 / type: complex / ID: 1 / Parent: 0
Details: Complex of recombinant Ebola virus glycoprotein and human IgG1 Fab ADI-15946 from a survivor.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #2: EBOV GPdMuc

SupramoleculeName: EBOV GPdMuc / type: complex / ID: 2 / Parent: 1
Details: Recombinant mucin-deleted Ebola virus glycoprotein expressed in mammalian cells, 293F.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F / Recombinant plasmid: pPPI4

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Supramolecule #3: ADI-15946 Fab

SupramoleculeName: ADI-15946 Fab / type: complex / ID: 3 / Parent: 1
Details: Fab fragment generated by proteolytic cleavage of IgG antibody, expressed in plant system.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Nicotiana benthamiana (plant)

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Supramolecule #4: ADI-15946 Fab

SupramoleculeName: ADI-15946 Fab / type: complex / ID: 4 / Parent: 1
Details: Fab fragment generated by proteolytic cleavage of IgG antibody, expressed in plant system.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Nicotiana benthamiana (plant)

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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

Concentration0.03 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTrisTris

Details: Solutions were made from a 10X stock and filtered sterilized.
StainingType: NEGATIVE / Material: Uranyl Formate
Details: Negatively stained EM specimens were prepared using a side-blotting technique and uranyl-formate stain.
GridModel: Protochip / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
DetailsMonodisperse sample deposited on negative stain grid.

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Number real images: 74 / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination 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

Particle selectionNumber selected: 11650
Startup modelType of model: OTHER
Details: Common lines start model obtained from negative stain class averages of the data.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 24.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN (ver. 2.2) / Number images used: 6677
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.2)
Final 3D classificationNumber classes: 82 / Avg.num./class: 50 / Software - Name: IMAGIC / Details: Iterative MSA/MRA

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