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- EMDB-7613: CryoEM structure of a neutralizing antibody Fab fragment bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-7613
TitleCryoEM structure of a neutralizing antibody Fab fragment bound to Zika Virus
Map dataCryoEM structure of a neutralizing antibody Fab fragment bound to Zika Virus
Sample
  • Complex: neutralizing antibody Fab fragment bound to Zika Virus
    • Complex: Fab fragment of a neutralizing Zika antibody
    • Virus: Zika virus
Biological speciesZika virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.7 Å
AuthorsSasisekharan R
CitationJournal: Cell Host Microbe / Year: 2018
Title: Rational Engineering and Characterization of an mAb that Neutralizes Zika Virus by Targeting a Mutationally Constrained Quaternary Epitope.
Authors: Kannan Tharakaraman / Satoru Watanabe / Kuan Rong Chan / Jia Huan / Vidya Subramanian / Yok Hian Chionh / Aditya Raguram / Devin Quinlan / Megan McBee / Eugenia Z Ong / Esther S Gan / Hwee ...Authors: Kannan Tharakaraman / Satoru Watanabe / Kuan Rong Chan / Jia Huan / Vidya Subramanian / Yok Hian Chionh / Aditya Raguram / Devin Quinlan / Megan McBee / Eugenia Z Ong / Esther S Gan / Hwee Cheng Tan / Anu Tyagi / Shashi Bhushan / Julien Lescar / Subhash G Vasudevan / Eng Eong Ooi / Ram Sasisekharan /
Abstract: Following the recent emergence of Zika virus (ZIKV), many murine and human neutralizing anti-ZIKV antibodies have been reported. Given the risk of virus escape mutants, engineering antibodies that ...Following the recent emergence of Zika virus (ZIKV), many murine and human neutralizing anti-ZIKV antibodies have been reported. Given the risk of virus escape mutants, engineering antibodies that target mutationally constrained epitopes with therapeutically relevant potencies can be valuable for combating future outbreaks. Here, we applied computational methods to engineer an antibody, ZAb_FLEP, that targets a highly networked and therefore mutationally constrained surface formed by the envelope protein dimer. ZAb_FLEP neutralized a breadth of ZIKV strains and protected mice in distinct in vivo models, including resolving vertical transmission and fetal mortality in infected pregnant mice. Serial passaging of ZIKV in the presence of ZAb_FLEP failed to generate viral escape mutants, suggesting that its epitope is indeed mutationally constrained. A single-particle cryo-EM reconstruction of the Fab-ZIKV complex validated the structural model and revealed insights into ZAb_FLEP's neutralization mechanism. ZAb_FLEP has potential as a therapeutic in future outbreaks.
History
DepositionMar 23, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseMay 9, 2018-
UpdateMay 9, 2018-
Current statusMay 9, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7613.png

Downloads & links

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Map

FileDownload / File: emd_7613.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of a neutralizing antibody Fab fragment bound to Zika Virus
Voxel sizeX=Y=Z: 1.28 Å
Density
Contour LevelBy AUTHOR: 0.0365 / Movie #1: 0.0365
Minimum - Maximum-0.090722546 - 0.29318857
Average (Standard dev.)0.00637322 (±0.025588332)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.281.281.28
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0910.2930.006

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Supplemental data

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Sample components

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Entire : neutralizing antibody Fab fragment bound to Zika Virus

EntireName: neutralizing antibody Fab fragment bound to Zika Virus
Components
  • Complex: neutralizing antibody Fab fragment bound to Zika Virus
    • Complex: Fab fragment of a neutralizing Zika antibody
    • Virus: Zika virus

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Supramolecule #1: neutralizing antibody Fab fragment bound to Zika Virus

SupramoleculeName: neutralizing antibody Fab fragment bound to Zika Virus
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Zika virus

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Supramolecule #2: Fab fragment of a neutralizing Zika antibody

SupramoleculeName: Fab fragment of a neutralizing Zika antibody / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Freestyle 293 cells

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Supramolecule #3: Zika virus

SupramoleculeName: Zika virus / type: virus / ID: 3 / Parent: 1 / NCBI-ID: 64320 / Sci species name: Zika virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 36.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8116

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 925

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