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- EMDB-5928: Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Int... -

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Entry
Database: EMDB / ID: EMD-5928
TitleKinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle
Map dataReconstruction of CVB3 A-particle transitioned by CAR
Sample
  • Sample: Coxsackievirus B3 A-Particle
  • Virus: Human coxsackievirus B3
Keywordscoxsackievirus b3 / cvb3 / CAR / cryoEM / A-particle
Biological speciesHuman coxsackievirus B3
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsOrgantini LJ / Makhov AM / Conway JF / Hafenstein S / Carson SD
CitationJournal: J Virol / Year: 2014
Title: Kinetic and structural analysis of coxsackievirus B3 receptor interactions and formation of the A-particle.
Authors: Lindsey J Organtini / Alexander M Makhov / James F Conway / Susan Hafenstein / Steven D Carson /
Abstract: The coxsackievirus and adenovirus receptor (CAR) has been identified as the cellular receptor for group B coxsackieviruses, including serotype 3 (CVB3). CAR mediates infection by binding to CVB3 and ...The coxsackievirus and adenovirus receptor (CAR) has been identified as the cellular receptor for group B coxsackieviruses, including serotype 3 (CVB3). CAR mediates infection by binding to CVB3 and catalyzing conformational changes in the virus that result in formation of the altered, noninfectious A-particle. Kinetic analyses show that the apparent first-order rate constant for the inactivation of CVB3 by soluble CAR (sCAR) at physiological temperatures varies nonlinearly with sCAR concentration. Cryo-electron microscopy (cryo-EM) reconstruction of the CVB3-CAR complex resulted in a 9.0-Å resolution map that was interpreted with the four available crystal structures of CAR, providing a consensus footprint for the receptor binding site. The analysis of the cryo-EM structure identifies important virus-receptor interactions that are conserved across picornavirus species. These conserved interactions map to variable antigenic sites or structurally conserved regions, suggesting a combination of evolutionary mechanisms for receptor site preservation. The CAR-catalyzed A-particle structure was solved to a 6.6-Å resolution and shows significant rearrangement of internal features and symmetric interactions with the RNA genome.
IMPORTANCE: This report presents new information about receptor use by picornaviruses and highlights the importance of attaining at least an ∼9-Å resolution for the interpretation of cryo-EM ...IMPORTANCE: This report presents new information about receptor use by picornaviruses and highlights the importance of attaining at least an ∼9-Å resolution for the interpretation of cryo-EM complex maps. The analysis of receptor binding elucidates two complementary mechanisms for preservation of the low-affinity (initial) interaction of the receptor and defines the kinetics of receptor-catalyzed conformational change to the A-particle.
History
DepositionMar 19, 2014-
Header (metadata) releaseApr 9, 2014-
Map releaseApr 9, 2014-
UpdateApr 30, 2014-
Current statusApr 30, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5928.gif

Downloads & links

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Map

FileDownload / File: emd_5928.map.gz / Format: CCP4 / Size: 161.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of CVB3 A-particle transitioned by CAR
Voxel sizeX=Y=Z: 1.25 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.51662302 - 6.65716362
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-175-175-175
Dimensions351351351
Spacing351351351
CellA=B=C: 438.75 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z351351351
origin x/y/z0.0000.0000.000
length x/y/z438.750438.750438.750
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-175-175-175
NC/NR/NS351351351
D min/max/mean-4.5176.657-0.000

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Supplemental data

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Sample components

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Entire : Coxsackievirus B3 A-Particle

EntireName: Coxsackievirus B3 A-Particle
Components
  • Sample: Coxsackievirus B3 A-Particle
  • Virus: Human coxsackievirus B3

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Supramolecule #1000: Coxsackievirus B3 A-Particle

SupramoleculeName: Coxsackievirus B3 A-Particle / type: sample / ID: 1000 / Details: purified virus and receptor complex in solution / Oligomeric state: icosahedral virus / Number unique components: 1
Molecular weightExperimental: 7 MDa

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Supramolecule #1: Human coxsackievirus B3

SupramoleculeName: Human coxsackievirus B3 / type: virus / ID: 1 / Name.synonym: CVB3
Details: Virus was incubated with excess CAR at 4 degrees C then transitioned to 37 degrees C in order to create the A-particle.
NCBI-ID: 12072 / Sci species name: Human coxsackievirus B3 / Sci species strain: CVB3/28 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: CVB3
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 7 MDa
Virus shellShell ID: 1 / Name: VP1-4 / 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

Concentration0.1 mg/mL
BufferpH: 6 / Details: 50 mM MES, 100 mM NaCl
GridDetails: glow-discharged holey carbon Quantifoil electron microscopy grids
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 95 % / Chamber temperature: 95 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 5.2 µm / Nominal defocus min: 2.33 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: CTFFIND3
DateAug 1, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 48 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: AUTO3DEM
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: EMAN, AUTO3DEM / Number images used: 41939
DetailsParticles were selected using EMAN.

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