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- EMDB-6794: Cryo-EM structure of zika virus complexed with Fab of a human mon... -

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Basic information

Entry
Database: EMDB / ID: EMD-6794
TitleCryo-EM structure of zika virus complexed with Fab of a human monoclonal antibody named ZKA190 at 4 degrees celsius
Map datazika virus complexed with Fab of a human monoclonal antibody named ZKA190 at 4 celsius degree
Sample
  • Complex: zika virus complexed with Fab molecule of a human monoclonal antibody named ZKA190
    • Complex: zika virus
    • Complex: Fab ZKA190
Biological speciesZika virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsWang JQ / Ng TS / Fibriansah G / Lok SM
CitationJournal: Cell / Year: 2017
Title: A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential.
Authors: Jiaqi Wang / Marco Bardelli / Diego A Espinosa / Mattia Pedotti / Thiam-Seng Ng / Siro Bianchi / Luca Simonelli / Elisa X Y Lim / Mathilde Foglierini / Fabrizia Zatta / Stefano Jaconi / ...Authors: Jiaqi Wang / Marco Bardelli / Diego A Espinosa / Mattia Pedotti / Thiam-Seng Ng / Siro Bianchi / Luca Simonelli / Elisa X Y Lim / Mathilde Foglierini / Fabrizia Zatta / Stefano Jaconi / Martina Beltramello / Elisabetta Cameroni / Guntur Fibriansah / Jian Shi / Taylor Barca / Isabel Pagani / Alicia Rubio / Vania Broccoli / Elisa Vicenzi / Victoria Graham / Steven Pullan / Stuart Dowall / Roger Hewson / Simon Jurt / Oliver Zerbe / Karin Stettler / Antonio Lanzavecchia / Federica Sallusto / Andrea Cavalli / Eva Harris / Shee-Mei Lok / Luca Varani / Davide Corti /
Abstract: Zika virus (ZIKV), a mosquito-borne flavivirus, causes devastating congenital birth defects. We isolated a human monoclonal antibody (mAb), ZKA190, that potently cross-neutralizes multi-lineage ZIKV ...Zika virus (ZIKV), a mosquito-borne flavivirus, causes devastating congenital birth defects. We isolated a human monoclonal antibody (mAb), ZKA190, that potently cross-neutralizes multi-lineage ZIKV strains. ZKA190 is highly effective in vivo in preventing morbidity and mortality of ZIKV-infected mice. NMR and cryo-electron microscopy show its binding to an exposed epitope on DIII of the E protein. ZKA190 Fab binds all 180 E protein copies, altering the virus quaternary arrangement and surface curvature. However, ZIKV escape mutants emerged in vitro and in vivo in the presence of ZKA190, as well as of other neutralizing mAbs. To counter this problem, we developed a bispecific antibody (FIT-1) comprising ZKA190 and a second mAb specific for DII of E protein. In addition to retaining high in vitro and in vivo potencies, FIT-1 robustly prevented viral escape, warranting its development as a ZIKV immunotherapy.
History
DepositionJul 15, 2017-
Header (metadata) releaseOct 4, 2017-
Map releaseOct 4, 2017-
UpdateOct 4, 2017-
Current statusOct 4, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6794.png

Downloads & links

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Map

FileDownload / File: emd_6794.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationzika virus complexed with Fab of a human monoclonal antibody named ZKA190 at 4 celsius degree
Voxel sizeX=Y=Z: 3.42 Å
Density
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-3.8800683 - 5.5665874
Average (Standard dev.)-0.000000000204838 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 684.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z684.000684.000684.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-3.8805.567-0.000

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Supplemental data

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Sample components

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Entire : zika virus complexed with Fab molecule of a human monoclonal anti...

EntireName: zika virus complexed with Fab molecule of a human monoclonal antibody named ZKA190
Components
  • Complex: zika virus complexed with Fab molecule of a human monoclonal antibody named ZKA190
    • Complex: zika virus
    • Complex: Fab ZKA190

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Supramolecule #1: zika virus complexed with Fab molecule of a human monoclonal anti...

SupramoleculeName: zika virus complexed with Fab molecule of a human monoclonal antibody named ZKA190
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Zika virus / Strain: H/PF/2013

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Supramolecule #2: zika virus

SupramoleculeName: zika virus / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Zika virus / Strain: H/PF/2013

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Supramolecule #3: Fab ZKA190

SupramoleculeName: Fab ZKA190 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: EXPI293

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
12.0 mMTris-HClTris
120.0 mMNaClSodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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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 / Cs: 2.7 mm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: ctffind3
Startup modelType of model: EMDB MAP
EMDB ID:

8139

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: Relion
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Relion
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Relion / Number images used: 10641
FSC plot (resolution estimation)

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