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- EMDB-5519: Electron cryo-tomography of coxsackievirus A9-integrin alpha v be... -

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Entry
Database: EMDB / ID: EMD-5519
TitleElectron cryo-tomography of coxsackievirus A9-integrin alpha v beta 6 complex
Map dataElectron cryo-tomography of coxsackievirus A9-integrin alpha v beta 6 complex
Sample
  • Sample: coxsackievirus A9 in complex with integrin alpha v beta 6
  • Virus: Human coxsackievirus A9
KeywordsCVA9-integrin / picornavirus / enterovirus / coxsackievirus A9 / integrin / tomography
Biological speciesHuman coxsackievirus A9
Methodelectron tomography / cryo EM
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 8, 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

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Supplemental images

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Map

FileDownload / File: emd_5519.map.gz / Format: CCP4 / Size: 227.2 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationElectron cryo-tomography of coxsackievirus A9-integrin alpha v beta 6 complex
Voxel sizeX=Y=Z: 7.68 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-37.194534300000001 (±113.802886959999995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-102-3430
Dimensions1824199667
Spacing1824199667
CellA: 15329.279 Å / B: 14008.319 Å / C: 514.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z7.6799994989987.67999945175447.68
M x/y/z1996182467
origin x/y/z0.0000.0000.000
length x/y/z15329.27914008.319514.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-34-10230
NC/NR/NS1996182467
D min/max/mean-128.000127.000-37.195

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Supplemental data

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Sample components

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Entire : coxsackievirus A9 in complex with integrin alpha v beta 6

EntireName: coxsackievirus A9 in complex with integrin alpha v beta 6
Components
  • Sample: coxsackievirus A9 in complex with integrin alpha v beta 6
  • Virus: Human coxsackievirus A9

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Supramolecule #1000: coxsackievirus A9 in complex with integrin alpha v beta 6

SupramoleculeName: coxsackievirus A9 in complex with integrin alpha v beta 6
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
Details: 10nm gold particles present in tomogram as fiducial.
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
Processingelectron tomography

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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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 / Nominal magnification: 39000
Sample stageSpecimen holder: GATAN 262 / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 3 °
DateJan 21, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC CCD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: IMOD / Number images used: 40

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