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- EMDB-2027: Coxsackievirus A7 (CAV7) empty capsid reconstruction at 6.09 angs... -

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Database: EMDB / ID: 2027
TitleCoxsackievirus A7 (CAV7) empty capsid reconstruction at 6.09 angstrom resolution.
Map dataThis is a three-dimensional model of coxsackievirus A7 (CAV7) at 6.09 angstrom resolution.
SampleCoxsackievirus A7 USSR-strain empty particles in buffer:
Keywordscoxsackievirus / CAV7 / picornavirus / enterovirus / HEV-A
Function / homologyPicornavirus capsid / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / picornavirus capsid protein / viral capsid / structural molecule activity / VP1 / VP2 / VP3
Function and homology information
SourceHuman coxsackievirus A7 (CAV7)
Methodsingle particle reconstruction / cryo EM / 6.09 Å resolution
AuthorsSeitsonen JJT / Shakeel S / Susi P / Pandurangan AP / Sinkovits RS / Hyvonen H / Laurinmaki P / Yla-Pelto J / Topf M / Hyypia T / Butcher SJ
CitationJournal: J. Virol. / Year: 2012
Title: Structural analysis of coxsackievirus A7 reveals conformational changes associated with uncoating.
Authors: Jani J T Seitsonen / Shabih Shakeel / Petri Susi / Arun P Pandurangan / Robert S Sinkovits / Heini Hyvönen / Pasi Laurinmäki / Jani Ylä-Pelto / Maya Topf / Timo Hyypiä / Sarah J Butcher
Validation ReportPDB-ID: 4biq

SummaryFull reportAbout validation report
DateDeposition: Jan 11, 2012 / Header (metadata) release: Mar 30, 2012 / Map release: Jun 11, 2012 / Last update: Apr 9, 2014

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 750
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 750
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-4biq
  • Surface level: 750
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-4biq
  • Surface level: 1400
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-4biq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

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Fileemd_2027.map.gz (map file in CCP4 format, 125941 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
401 pix
1.13 Å/pix.
= 453.13 Å
401 pix
1.13 Å/pix.
= 453.13 Å
401 pix
1.13 Å/pix.
= 453.13 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Contour Level:750 (by author), 750 (movie #1):
Minimum - Maximum-2101.00000000 - 3670.00000000
Average (Standard dev.)0.30472371 (499.74902344)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 453.13 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.131.131.13
M x/y/z401401401
origin x/y/z0.0000.0000.000
length x/y/z453.130453.130453.130
start NX/NY/NZ-184-184-183
MAP C/R/S123
start NC/NR/NS-200-200-200
D min/max/mean-2101.0003670.0000.305

Supplemental data

Sample components

Entire Coxsackievirus A7 USSR-strain empty particles in buffer

EntireName: Coxsackievirus A7 USSR-strain empty particles in buffer
Number of components: 1 / Oligomeric State: empty particle (no RNA)
MassTheoretical: 5.2 MDa

Component #1: virus, Human coxsackievirus A7

VirusName: Human coxsackievirus A7 / a.k.a: CAV7 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 5.2 MDa
SpeciesSpecies: Human coxsackievirus A7 (CAV7)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: VP1VP2VP3 / Diameter: 300 Å / T number(triangulation number): 1

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / Buffer solution: 25 mM phosphate buffer, 0.5 mM MgCl2 / pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: Manual / Details: Vitrification instrument: Custom built

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 62000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 620 - 4810 nm
Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 264 / Scanner: OTHER / Sampling size: 7 microns / Details: Scanned with Zeiss Photoscan TD

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7849 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Fourier / Software: AUTO3DEM / CTF correction: Each micrograph / Resolution: 6.09 Å / Resolution method: FSC 0.5

Atomic model buiding

Output model

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