[English] 日本語
Yorodumi
- EMDB-0173: Complex of foot-and-mouth-disease virus (type O1 M) with the Fab ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0173
TitleComplex of foot-and-mouth-disease virus (type O1 M) with the Fab of antibody D9. The virus is at 3.5 Ang resolution, the Fab is flexibly attached and at much lower resolution.
Map data
Sample
  • Virus: Foot-and-mouth disease virus in complex with D9 FAB
    • Complex: Foot-and-mouth disease virus
    • Complex: D9 FAB
Biological speciesFoot-and-mouth disease virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsShimmon G / Kotecha A / Ren J / Asfor AS / Newman J / Berryman S / Cottam EM / Gold S / Tuthill TJ / King DP ...Shimmon G / Kotecha A / Ren J / Asfor AS / Newman J / Berryman S / Cottam EM / Gold S / Tuthill TJ / King DP / Brocchi E / King AMQ / Owens R / Fry EE / Stuart DI / Burman A / Jackson T
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000099 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
Medical Research Council (United Kingdom)G1100525/1 United Kingdom
CitationJournal: PLoS One / Year: 2018
Title: Generation and characterisation of recombinant FMDV antibodies: Applications for advancing diagnostic and laboratory assays.
Authors: Gareth Shimmon / Abhay Kotecha / Jingshan Ren / Amin S Asfor / Joseph Newman / Stephen Berryman / Eleanor M Cottam / Sarah Gold / Toby J Tuthill / Donald P King / Emiliana Brocchi / Andrew M ...Authors: Gareth Shimmon / Abhay Kotecha / Jingshan Ren / Amin S Asfor / Joseph Newman / Stephen Berryman / Eleanor M Cottam / Sarah Gold / Toby J Tuthill / Donald P King / Emiliana Brocchi / Andrew M Q King / Ray Owens / Elizabeth E Fry / David I Stuart / Alison Burman / Terry Jackson /
Abstract: Foot-and-mouth disease (FMD) affects economically important livestock and is one of the most contagious viral diseases. The most commonly used FMD diagnostic assay is a sandwich ELISA. However, the ...Foot-and-mouth disease (FMD) affects economically important livestock and is one of the most contagious viral diseases. The most commonly used FMD diagnostic assay is a sandwich ELISA. However, the main disadvantage of this ELISA is that it requires anti-FMD virus (FMDV) serotype-specific antibodies raised in small animals. This problem can be, in part, overcome by using anti-FMDV monoclonal antibodies (MAbs) as detecting reagents. However, the long-term use of MAbs may be problematic and they may need to be replaced. Here we have constructed chimeric antibodies (mouse/rabbit D9) and Fabs (fragment antigen-binding) (mouse/cattle D9) using the Fv (fragment variable) regions of a mouse MAb, D9 (MAb D9), which recognises type O FMDV. The mouse/rabbit D9 chimeric antibody retained the FMDV serotype-specificity of MAb D9 and performed well in a FMDV detection ELISA as well as in routine laboratory assays. Cryo-electron microscopy analysis confirmed engagement with antigenic site 1 and peptide competition studies identified the aspartic acid at residue VP1 147 as a novel component of the D9 epitope. This chimeric expression approach is a simple but effective way to preserve valuable FMDV antibodies, and has the potential for unlimited generation of antibodies and antibody fragments in recombinant systems with the concomitant positive impacts on the 3Rs (Replacement, Reduction and Refinement) principles.
History
DepositionAug 2, 2018-
Header (metadata) releaseAug 29, 2018-
Map releaseAug 29, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0425
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0425
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0173.png

Downloads & links

-
Map

FileDownload / File: emd_0173.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.0425 / Movie #1: 0.0425
Minimum - Maximum-0.10880451 - 0.18983106
Average (Standard dev.)0.0011324808 (±0.012099084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-3990
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-39900
NC/NR/NS400400400
D min/max/mean-0.1090.1900.001

-
Supplemental data

-
Additional map: This is unsharpened map where the density of...

Fileemd_0173_additional.map
AnnotationThis is unsharpened map where the density of flexible Fabs are visible.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Foot-and-mouth disease virus in complex with D9 FAB

EntireName: Foot-and-mouth disease virus in complex with D9 FAB
Components
  • Virus: Foot-and-mouth disease virus in complex with D9 FAB
    • Complex: Foot-and-mouth disease virus
    • Complex: D9 FAB

-
Supramolecule #1: Foot-and-mouth disease virus in complex with D9 FAB

SupramoleculeName: Foot-and-mouth disease virus in complex with D9 FAB / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 9 MDa
Virus shellShell ID: 1 / Name: Foot and Mouth Disease virus / Diameter: 300.0 Å / T number (triangulation number): 3

-
Supramolecule #2: Foot-and-mouth disease virus

SupramoleculeName: Foot-and-mouth disease virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Foot-and-mouth disease virus
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)

-
Supramolecule #3: D9 FAB

SupramoleculeName: D9 FAB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Component - Concentration: 50.0 mM / Component - Name: HEPES
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 160000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 360 / Average exposure time: 5.0 sec. / Average electron dose: 18.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0.17)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1bbt

Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)
Final angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.3)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 1003

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 120 / Target criteria: Cross-correlation coefficient

+
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