|Entry||Database: EMDB / ID: EMD-5928|
|Title||Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle|
|Sample||Coxsackievirus B3 A-Particle:|
|Keywords||coxsackievirus b3 / cvb3 / CAR / cryoEM / A-particle|
|Biological species||Human coxsackievirus B3 (CVB3)|
|Method||single particle reconstruction / cryo EM / Resolution: 9 Å|
|Authors||Organtini LJ / Makhov AM / Conway JF / Hafenstein S / Carson SD|
|Citation||Journal: 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.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_5928.map.gz / Format: CCP4 / Size: 161.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.25 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Coxsackievirus B3 A-Particle
|Entire||Name: Coxsackievirus B3 A-Particle / Details: purified virus and receptor complex in solution / Number of components: 1 / Oligomeric State: icosahedral virus|
|Mass||Experimental: 7 MDa|
-Component #1: virus, Human coxsackievirus B3
|Virus||Name: Human coxsackievirus B3 / a.k.a: CVB3 / Class: VIRION|
Details: Virus was incubated with excess CAR at 4 degrees C then transitioned to 37 degrees C in order to create the A-particle.
Empty: No / Enveloped: No / Isolate: STRAIN
|Mass||Experimental: 7 MDa|
|Species||Species: Human coxsackievirus B3 (CVB3) / Strain: CVB3/28|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Shell #1||Name of element: VP1-4 / Diameter: 300 Å / T number (triangulation number): 1|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.1 mg/mL / Buffer solution: 50 mM MES, 100 mM NaCl / pH: 6|
|Support film||glow-discharged holey carbon Quantifoil electron microscopy grids|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 95 K / Humidity: 95 %|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Aug 1, 2012|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: CTFFIND3 / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2330 - 5200 nm|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 48 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 µm|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 41939 / Details: Particles were selected using EMAN.|
|3D reconstruction||Algorithm: Common Lines / Software: EMAN, AUTO3DEM / CTF correction: AUTO3DEM / Resolution: 9 Å / Resolution method: FSC 0.5, semi-independent|
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