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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: 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
Samplezika virus complexed with Fab molecule of a human monoclonal antibody named ZKA190:
zika virus / Fab ZKA190
SourceZika virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 22 Å resolution
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 / 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.
DateDeposition: Jul 15, 2017 / Header (metadata) release: Oct 4, 2017 / Map release: Oct 4, 2017 / Last update: Oct 4, 2017

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Structure visualization

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

Downloads & links

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Map

Fileemd_6794.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
3.42 Å/pix.
= 684. Å
200 pix
3.42 Å/pix.
= 684. Å
200 pix
3.42 Å/pix.
= 684. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-3.8800683 - 5.5665874
Average (Standard dev.)-2.04838E-10 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 684 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
Number of components: 3

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Component #1: protein, zika virus complexed with Fab molecule of a human monocl...

ProteinName: zika virus complexed with Fab molecule of a human monoclonal antibody named ZKA190
Recombinant expression: No
SourceSpecies: Zika virus / Strain: H/PF/2013
Source (engineered)Expression System: Zika virus

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Component #2: protein, zika virus

ProteinName: zika virus / Recombinant expression: No
SourceSpecies: Zika virus / Strain: H/PF/2013
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: EXPI293

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Component #3: protein, Fab ZKA190

ProteinName: Fab ZKA190 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: EXPI293

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 10641
3D reconstructionSoftware: Relion / Resolution: 22 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot
(resolution estimation)

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