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- EMDB-2028: Coxsackievirus A7 (CAV7) full capsid reconstruction at 8.23 angst... -

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Basic information

Entry
Database: EMDB / ID: EMD-2028
TitleCoxsackievirus A7 (CAV7) full capsid reconstruction at 8.23 angstrom resolution.
Map dataThis a three-dimensional reconstruction of coxsackievirus A7 (CAV7) at 8.23 angstrom resolution.
Sample
  • Sample: Coxsackievirus A7 USSR-strain native particles in buffer
  • Virus: Human coxsackievirus A7
Keywordscoxsackievirus / CAV7 / picornavirus / enterovirus / HEV-A
Function / homology
Function and homology information


viral capsid / symbiont entry into host cell / structural molecule activity / virion attachment to host cell
Similarity search - Function
Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus A7
Methodsingle particle reconstruction / cryo EM / Resolution: 8.23 Å
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 /
Abstract: Coxsackievirus A7 (CAV7) is a rarely detected and poorly characterized serotype of the Enterovirus species Human enterovirus A (HEV-A) within the Picornaviridae family. The CAV7-USSR strain has ...Coxsackievirus A7 (CAV7) is a rarely detected and poorly characterized serotype of the Enterovirus species Human enterovirus A (HEV-A) within the Picornaviridae family. The CAV7-USSR strain has caused polio-like epidemics and was originally thought to represent the fourth poliovirus type, but later evidence linked this strain to the CAV7-Parker prototype. Another isolate, CAV7-275/58, was also serologically similar to Parker but was noninfectious in a mouse model. Sequencing of the genomic region encoding the capsid proteins of the USSR and 275/58 strains and subsequent comparison with the corresponding amino acid sequences of the Parker strain revealed that the Parker and USSR strains are nearly identical, while the 275/58 strain is more distant. Using electron cryomicroscopy and three-dimensional image reconstruction, the structures of the CAV7-USSR virion and empty capsid were resolved to 8.2-Å and 6.1-Å resolutions, respectively. This is one of the first detailed structural analyses of the HEV-A species. Using homology modeling, reconstruction segmentation, and flexible fitting, we constructed a pseudoatomic T = 1 (pseudo T = 3) model incorporating the three major capsid proteins (VP1 to VP3), addressed the conformational changes of the capsid and its constituent viral proteins occurring during RNA release, and mapped the capsid proteins' variable regions to the structure. During uncoating, VP4 and RNA are released analogously to poliovirus 1, the interfaces of VP2 and VP3 are rearranged, and VP1 rotates. Variable regions in the capsid proteins were predicted to map mainly to the surface of VP1 and are thus likely to affect the tropism and pathogenicity of CAV7.
History
DepositionJan 11, 2012-
Header (metadata) releaseMar 30, 2012-
Map releaseJun 11, 2012-
UpdateApr 2, 2014-
Current statusApr 2, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • 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-4bip
  • Surface level: 750
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4bip
  • Surface level: 750
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4bip
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EM-2028.tif

Downloads & links

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Map

FileDownload / File: emd_2028.map.gz / Format: CCP4 / Size: 120.1 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThis a three-dimensional reconstruction of coxsackievirus A7 (CAV7) at 8.23 angstrom resolution.
Voxel sizeX=Y=Z: 1.13 Å
Density
Contour LevelBy AUTHOR: 750.0 / Movie #1: 750
Minimum - Maximum-1647.0 - 3167.0
Average (Standard dev.)0.39889425 (±499.69790648999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions401401401
Spacing401401401
CellA=B=C: 453.13 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS401401401
D min/max/mean-1647.0003167.0000.399

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Supplemental data

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Sample components

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Entire : Coxsackievirus A7 USSR-strain native particles in buffer

EntireName: Coxsackievirus A7 USSR-strain native particles in buffer
Components
  • Sample: Coxsackievirus A7 USSR-strain native particles in buffer
  • Virus: Human coxsackievirus A7

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Supramolecule #1000: Coxsackievirus A7 USSR-strain native particles in buffer

SupramoleculeName: Coxsackievirus A7 USSR-strain native particles in buffer
type: sample / ID: 1000 / Oligomeric state: full particle / Number unique components: 1
Molecular weightTheoretical: 5.7 MDa

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Supramolecule #1: Human coxsackievirus A7

SupramoleculeName: Human coxsackievirus A7 / type: virus / ID: 1 / Name.synonym: CAV7 / NCBI-ID: 42787 / Sci species name: Human coxsackievirus A7 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: CAV7
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 5.7 MDa
Virus shellShell ID: 1 / Name: VP1VP2VP3VP4 / Diameter: 300 Å / T number (triangulation number): 1

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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

Concentration3 mg/mL
BufferpH: 7.4 / Details: 25 mM phosphate buffer, 0.5 mM MgCl2
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Custom built / Method: Manual

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.81 µm / Nominal defocus min: 0.62 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 223 / Average electron dose: 17 e/Å2 / Details: Scanned with Zeiss Photoscan TD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.23 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 2152

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