[English] 日本語
Yorodumi
- EMDB-7613: CryoEM structure of a neutralizing antibody Fab fragment bound to... -

+
Open data


ID or keywords:

Loading...

-
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

-
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

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 200 pix.
= 256. Å		1.28 Å/pix.
x 200 pix.
= 256. Å		1.28 Å/pix.
x 200 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28 Å
Density

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8116

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more