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- EMDB-5514: Icosahedral reconstruction of empty coxsackievirus A9 capsid-inte... -

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Basic information

Entry
Database: EMDB / ID: EMD-5514
TitleIcosahedral reconstruction of empty coxsackievirus A9 capsid-integrin alpha v beta 6 complex
Map dataIcosahedral reconstruction of empty coxsackievirus A9 capsid-integrin alpha v beta 6 complex
Sample
  • Sample: empty coxsackievirus A9 capsid in complex with integrin alpha v beta 6
  • Virus: Human coxsackievirus A9
KeywordsCVA9-integrin / picornavirus / enterovirus / coxsackievirus A9 / integrin / empty capsid
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHuman coxsackievirus A9
Methodsingle particle reconstruction / cryo EM / Resolution: 9.54 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-
UpdateAug 14, 2013-
Current statusAug 14, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 300
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 300
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2j
  • Surface level: 17000
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2j
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5514_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5514.map.gz / Format: CCP4 / Size: 15.1 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationIcosahedral reconstruction of empty coxsackievirus A9 capsid-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 EMDB: 3000.0 / Movie #1: 300
Minimum - Maximum0.0 - 32767.0
Average (Standard dev.)1849.604492189999974 (±5100.455566409999847)
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 Integer*27
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/mean0.00032767.0001849.604

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Supplemental data

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Sample components

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

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

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

SupramoleculeName: empty coxsackievirus A9 capsid 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 / NCBI-ID: 12067 / Sci species name: Human coxsackievirus A9 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / 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 / Method: manual plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
DateFeb 1, 2011
Image recordingDigitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 147
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: 4.12 µm / Nominal defocus min: 0.83 µm / Nominal magnification: 62000
Sample stageSpecimen holder: GATAN 626 / 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: 9.54 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 1200

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Atomic model buiding 1

Initial modelPDB ID:

1d4m


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: imodfit
DetailsProtocol: flexible fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j2j:
Empty coxsackievirus A9 capsid

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