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- EMDB-3311: Cryo-EM structure of Ebola GP-Fab100-Fab114 ternary complex at pH 5 -

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Basic information

Entry
Database: EMDB / ID: EMD-3311
TitleCryo-EM structure of Ebola GP-Fab100-Fab114 ternary complex at pH 5
Map dataCryo-EM reconstruction of Ebola GP-Fab100-Fab114 ternary complex at pH 5
Sample
  • Sample: Ebola GP binds to Fab Fragments of mAb100 and mAb114
  • Protein or peptide: Ebola virus glycoprotein
  • Protein or peptide: mAb100
  • Protein or peptide: mAb114
KeywordsEbola virus neutralization antibody
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsMisasi J / Gilman M / Kanekiyo M / Gui M / Cagigi A / Mulangu S / Corti D / Ledgerwood J / Lanzavecchia A / Cunningham J ...Misasi J / Gilman M / Kanekiyo M / Gui M / Cagigi A / Mulangu S / Corti D / Ledgerwood J / Lanzavecchia A / Cunningham J / Muyembe-Tamfun J / Baxa U / Graham B / Xiang Y / Sullivan N / McLellan J
CitationJournal: Science / Year: 2016
Title: Structural and molecular basis for Ebola virus neutralization by protective human antibodies.
Authors: John Misasi / Morgan S A Gilman / Masaru Kanekiyo / Miao Gui / Alberto Cagigi / Sabue Mulangu / Davide Corti / Julie E Ledgerwood / Antonio Lanzavecchia / James Cunningham / Jean Jacques ...Authors: John Misasi / Morgan S A Gilman / Masaru Kanekiyo / Miao Gui / Alberto Cagigi / Sabue Mulangu / Davide Corti / Julie E Ledgerwood / Antonio Lanzavecchia / James Cunningham / Jean Jacques Muyembe-Tamfun / Ulrich Baxa / Barney S Graham / Ye Xiang / Nancy J Sullivan / Jason S McLellan /
Abstract: Ebola virus causes hemorrhagic fever with a high case fatality rate for which there is no approved therapy. Two human monoclonal antibodies, mAb100 and mAb114, in combination, protect nonhuman ...Ebola virus causes hemorrhagic fever with a high case fatality rate for which there is no approved therapy. Two human monoclonal antibodies, mAb100 and mAb114, in combination, protect nonhuman primates against all signs of Ebola virus disease, including viremia. Here, we demonstrate that mAb100 recognizes the base of the Ebola virus glycoprotein (GP) trimer, occludes access to the cathepsin-cleavage loop, and prevents the proteolytic cleavage of GP that is required for virus entry. We show that mAb114 interacts with the glycan cap and inner chalice of GP, remains associated after proteolytic removal of the glycan cap, and inhibits binding of cleaved GP to its receptor. These results define the basis of neutralization for two protective antibodies and may facilitate development of therapies and vaccines.
History
DepositionJan 29, 2016-
Header (metadata) releaseFeb 24, 2016-
Map releaseMar 2, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0213
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0213
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3311.jpg

Downloads & links

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Map

FileDownload / File: emd_3311.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of Ebola GP-Fab100-Fab114 ternary complex at pH 5
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.0213 / Movie #1: 0.0213
Minimum - Maximum-0.05702131 - 0.09657204
Average (Standard dev.)0.00038889 (±0.00414544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0570.0970.000

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Supplemental data

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Sample components

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Entire : Ebola GP binds to Fab Fragments of mAb100 and mAb114

EntireName: Ebola GP binds to Fab Fragments of mAb100 and mAb114
Components
  • Sample: Ebola GP binds to Fab Fragments of mAb100 and mAb114
  • Protein or peptide: Ebola virus glycoprotein
  • Protein or peptide: mAb100
  • Protein or peptide: mAb114

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Supramolecule #1000: Ebola GP binds to Fab Fragments of mAb100 and mAb114

SupramoleculeName: Ebola GP binds to Fab Fragments of mAb100 and mAb114 / type: sample / ID: 1000
Oligomeric state: One trimer of Ebola GP binds to three fab fragments of mAb100 and three fab fragments of mAb114
Number unique components: 3
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: Ebola virus glycoprotein

MacromoleculeName: Ebola virus glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: GP / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Zaire ebolavirus / Strain: Mayinga / synonym: Ebola virus
SequenceUniProtKB: Envelope glycoprotein

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Macromolecule #2: mAb100

MacromoleculeName: mAb100 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293Freestyle cells / Recombinant plasmid: CMV/R type and VRC8400

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Macromolecule #3: mAb114

MacromoleculeName: mAb114 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293Freestyle cells / Recombinant plasmid: CMV/R type and VRC8400

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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

Concentration0.1 mg/mL
BufferpH: 5
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateMar 26, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 8793
FSC plot (resolution estimation)

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