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- EMDB-0173: Complex of foot-and-mouth-disease virus (type O1 M) with the Fab ... -

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Basic information

Database: EMDB / ID: 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
SampleFoot-and-mouth disease virus in complex with D9 FAB:
virus / Foot-and-mouth disease virus / D9 FAB
SourceFoot-and-mouth disease virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.97 Å resolution
AuthorsShimmon 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
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 Q King / Ray Owens / Elizabeth E Fry / David I Stuart / Alison Burman / Terry Jackson
DateDeposition: Aug 2, 2018 / Header (metadata) release: Aug 29, 2018 / Map release: Aug 29, 2018 / Last update: Aug 29, 2018

Structure visualization

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

Downloads & links


Fileemd_0173.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.35 Å/pix.
= 540. Å
400 pix
1.35 Å/pix.
= 540. Å
400 pix
1.35 Å/pix.
= 540. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Contour Level:0.0425 (by author), 0.0425 (movie #1):
Minimum - Maximum-0.10880451 - 0.18983106
Average (Standard dev.)0.0011324808 (0.012099084)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 540.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-39900
D min/max/mean-0.1090.1900.001

Supplemental data

Sample components

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

EntireName: Foot-and-mouth disease virus in complex with D9 FAB / Number of components: 3

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

VirusName: Foot-and-mouth disease virus in complex with D9 FAB / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE
MassTheoretical: 9 MDa
Source (natural)Host Species: Bos taurus (cattle)
Shell #1Name of element: Foot and Mouth Disease virus / Diameter: 300.0 Å / T number(triangulation number): 3

Component #2: protein, Foot-and-mouth disease virus

ProteinName: Foot-and-mouth disease virus / Recombinant expression: No
SourceSpecies: Foot-and-mouth disease virus
Source (engineered)Expression System: Cricetinae gen. sp. (mammal)

Component #3: protein, D9 FAB

ProteinName: D9 FAB / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 294 K / Humidity: 90 %

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 160000. X (nominal), 37037. X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 4000.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 70.0 - 70.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 360

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 1003
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 12

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