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- EMDB-5517: Asymmetric reconstruction of filled-integrin alpha v beta 6 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-5517
TitleAsymmetric reconstruction of filled-integrin alpha v beta 6 complex
Map dataAsymmetric reconstruction of filled-integrin alpha v beta 6 complex
Sample
  • Sample: asymmetric reconstruction of filled-integrin alpha v beta 6 complex
  • Virus: Human coxsackievirus A9
KeywordsCVA9-integrin / picornavirus / enterovirus / coxsackievirus A9 / integrin / asymmetric reconstruction
Biological speciesHuman coxsackievirus A9
Methodsingle particle reconstruction / cryo EM / Resolution: 28.2 Å
AuthorsShakeel S / Seitsonen JJT / Kajander T / Laurinmaki P / Hyypia T / Susi P / Butcher SJ
CitationJournal: J Virol / Year: 2013
Title: Structural and functional analysis of coxsackievirus A9 integrin αvβ6 binding and uncoating.
Authors: Shabih Shakeel / Jani J T Seitsonen / Tommi Kajander / Pasi Laurinmäki / Timo Hyypiä / Petri Susi / Sarah J Butcher /
Abstract: Coxsackievirus A9 (CVA9) is an important pathogen of the Picornaviridae family. It utilizes cellular receptors from the integrin αv family for binding to its host cells prior to entry and genome ...Coxsackievirus A9 (CVA9) is an important pathogen of the Picornaviridae family. It utilizes cellular receptors from the integrin αv family for binding to its host cells prior to entry and genome release. Among the integrins tested, it has the highest affinity for αvβ6, which recognizes the arginine-glycine-aspartic acid (RGD) loop present on the C terminus of viral capsid protein, VP1. As the atomic model of CVA9 lacks the RGD loop, we used surface plasmon resonance, electron cryo-microscopy, and image reconstruction to characterize the capsid-integrin interactions and the conformational changes on genome release. We show that the integrin binds to the capsid with nanomolar affinity and that the binding of integrin to the virion does not induce uncoating, thereby implying that further steps are required for release of the genome. Electron cryo-tomography and single-particle image reconstruction revealed variation in the number and conformation of the integrins bound to the capsid, with the integrin footprint mapping close to the predicted site for the exposed RGD loop on VP1. Comparison of empty and RNA-filled capsid reconstructions showed that the capsid undergoes conformational changes when the genome is released, so that the RNA-capsid interactions in the N termini of VP1 and VP4 are lost, VP4 is removed, and the capsid becomes more porous, as has been reported for poliovirus 1, human rhinovirus 2, enterovirus 71, and coxsackievirus A7. These results are important for understanding the structural basis of integrin binding to CVA9 and the molecular events leading to CVA9 cell entry and uncoating.
History
DepositionOct 4, 2012-
Header (metadata) releaseJul 3, 2013-
Map releaseJul 17, 2013-
UpdateJul 17, 2013-
Current statusJul 17, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5517_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5517.map.gz / Format: CCP4 / Size: 30.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction of filled-integrin alpha v beta 6 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 201 pix.
= 454.26 Å		2.26 Å/pix.
x 201 pix.
= 454.26 Å		2.26 Å/pix.
x 201 pix.
= 454.26 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-2.88894749 - 4.88957167
Average (Standard dev.)0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions201201201
Spacing201201201
CellA=B=C: 454.26 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.262.262.26
M x/y/z201201201
origin x/y/z0.0000.0000.000
length x/y/z454.260454.260454.260
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS201201201
D min/max/mean-2.8894.8900.000

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Supplemental data

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Sample components

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Entire : asymmetric reconstruction of filled-integrin alpha v beta 6 complex

EntireName: asymmetric reconstruction of filled-integrin alpha v beta 6 complex
Components
  • Sample: asymmetric reconstruction of filled-integrin alpha v beta 6 complex
  • Virus: Human coxsackievirus A9

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Supramolecule #1000: asymmetric reconstruction of filled-integrin alpha v beta 6 complex

SupramoleculeName: asymmetric reconstruction of filled-integrin alpha v beta 6 complex
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Human coxsackievirus A9

SupramoleculeName: Human coxsackievirus A9 / type: virus / ID: 1 / Name.synonym: CVA9 / NCBI-ID: 12067 / Sci species name: Human coxsackievirus A9 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: CVA9
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / 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

VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TECNAI F20
DateMar 1, 2012
Image recordingDigitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 64
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.54 µm / Nominal defocus min: 0.83 µm / Nominal magnification: 62000
Sample stageSpecimen holder: GATAN 262 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: whole micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 1

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