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- EMDB-6150: Structures of Protective Antibodies Reveal Sites of Vulnerability... -

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Entry
Database: EMDB / ID: EMD-6150
TitleStructures of Protective Antibodies Reveal Sites of Vulnerability on Ebola Virus
Map dataReconstruction of Ebola virus glycoprotein in complex with Fab fragments of c1H3 and KZ52
Sample
  • Sample: Complex of Ebola virus glycoprotein with transmembrane region and cytoplasmic tail removed (GPdTM) in complex with Fab fragments of c1H3 chimerized human IgG1 and human KZ52 IgG1 antibodies to Ebola virus GP
  • Protein or peptide: Ebola virus GP
  • Protein or peptide: chimerized human IgG1 antigen binding fragment c1H3
  • Protein or peptide: chimerized human IgG1 antigen binding fragment KZ52
KeywordsEbola / Antibody cocktails / mAbs / ZMAb / ZMapp / MB-003
Biological speciesEbola virus sp. / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsMurin CD / Fusco ML / Bornholdt ZA / Qiu X / Olinger GG / Zeitlin L / Kobinger GP / Ward AB / Saphire EO
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Structures of protective antibodies reveal sites of vulnerability on Ebola virus.
Authors: Charles D Murin / Marnie L Fusco / Zachary A Bornholdt / Xiangguo Qiu / Gene G Olinger / Larry Zeitlin / Gary P Kobinger / Andrew B Ward / Erica Ollmann Saphire /
Abstract: Ebola virus (EBOV) and related filoviruses cause severe hemorrhagic fever, with up to 90% lethality, and no treatments are approved for human use. Multiple recent outbreaks of EBOV and the likelihood ...Ebola virus (EBOV) and related filoviruses cause severe hemorrhagic fever, with up to 90% lethality, and no treatments are approved for human use. Multiple recent outbreaks of EBOV and the likelihood of future human exposure highlight the need for pre- and postexposure treatments. Monoclonal antibody (mAb) cocktails are particularly attractive candidates due to their proven postexposure efficacy in nonhuman primate models of EBOV infection. Two candidate cocktails, MB-003 and ZMAb, have been extensively evaluated in both in vitro and in vivo studies. Recently, these two therapeutics have been combined into a new cocktail named ZMapp, which showed increased efficacy and has been given compassionately to some human patients. Epitope information and mechanism of action are currently unknown for most of the component mAbs. Here we provide single-particle EM reconstructions of every mAb in the ZMapp cocktail, as well as additional antibodies from MB-003 and ZMAb. Our results illuminate key and recurring sites of vulnerability on the EBOV glycoprotein and provide a structural rationale for the efficacy of ZMapp. Interestingly, two of its components recognize overlapping epitopes and compete with each other for binding. Going forward, this work now provides a basis for strategic selection of next-generation antibody cocktails against Ebola and related viruses and a model for predicting the impact of ZMapp on potential escape mutations in ongoing or future Ebola outbreaks.
History
DepositionOct 25, 2014-
Header (metadata) releaseNov 19, 2014-
Map releaseNov 19, 2014-
UpdateDec 10, 2014-
Current statusDec 10, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6150.jpg

Downloads & links

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Map

FileDownload / File: emd_6150.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Ebola virus glycoprotein in complex with Fab fragments of c1H3 and KZ52
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: 3.55 / Movie #1: 3.55
Minimum - Maximum-4.40797615 - 13.05906105
Average (Standard dev.)0.00428074 (±0.99983615)
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
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-4.40813.0590.004

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Supplemental data

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Sample components

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Entire : Complex of Ebola virus glycoprotein with transmembrane region and...

EntireName: Complex of Ebola virus glycoprotein with transmembrane region and cytoplasmic tail removed (GPdTM) in complex with Fab fragments of c1H3 chimerized human IgG1 and human KZ52 IgG1 antibodies to Ebola virus GP
Components
  • Sample: Complex of Ebola virus glycoprotein with transmembrane region and cytoplasmic tail removed (GPdTM) in complex with Fab fragments of c1H3 chimerized human IgG1 and human KZ52 IgG1 antibodies to Ebola virus GP
  • Protein or peptide: Ebola virus GP
  • Protein or peptide: chimerized human IgG1 antigen binding fragment c1H3
  • Protein or peptide: chimerized human IgG1 antigen binding fragment KZ52

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Supramolecule #1000: Complex of Ebola virus glycoprotein with transmembrane region and...

SupramoleculeName: Complex of Ebola virus glycoprotein with transmembrane region and cytoplasmic tail removed (GPdTM) in complex with Fab fragments of c1H3 chimerized human IgG1 and human KZ52 IgG1 antibodies to Ebola virus GP
type: sample / ID: 1000
Oligomeric state: Ebola GP trimer bound to six Fab fragments (two per monomer)
Number unique components: 3
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: Ebola virus GP

MacromoleculeName: Ebola virus GP / type: protein_or_peptide / ID: 1 / Name.synonym: EBOV GP / Details: transmembrane and cytoplasmic tail removed / Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Ebola virus sp.
Molecular weightTheoretical: 450 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly) / Recombinant cell: Schneider 2 (S2) / Recombinant plasmid: pMT-puro

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Macromolecule #2: chimerized human IgG1 antigen binding fragment c1H3

MacromoleculeName: chimerized human IgG1 antigen binding fragment c1H3 / type: protein_or_peptide / ID: 2 / Name.synonym: c1H3 Fab / Number of copies: 3 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Nicotiana benthamiana (plant)

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Macromolecule #3: chimerized human IgG1 antigen binding fragment KZ52

MacromoleculeName: chimerized human IgG1 antigen binding fragment KZ52 / type: protein_or_peptide / ID: 3 / Name.synonym: KZ52 Fab / Number of copies: 3 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: 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 / Details: 20 mM Tris, 150 mM NaCl
StainingType: NEGATIVE
Details: To prepare negative stain grids, a 4 uL aliquot of each complex, which had been diluted to a concentration of ~0.03 ug/mL with TBS buffer, was placed for 15 seconds onto carbon-coated 400 Cu ...Details: To prepare negative stain grids, a 4 uL aliquot of each complex, which had been diluted to a concentration of ~0.03 ug/mL with TBS buffer, was placed for 15 seconds onto carbon-coated 400 Cu mesh grids that had been plasma cleaned for 20 s (Gatan), blotted off on the edge of the grid, then immediately stained for 30 s with 4 uL of 2% uranyl formate. The stain was blotted off on the edge of the grid and the grid was allowed to dry.
GridDetails: 400 Cu mesh grids, plasma-cleaned with Ag/O2 mix for 20 seconds
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 15, 2014
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 23
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles selected and sorted using automatic selection program (DoG Picker, Xmipp) using Appion.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 2411

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