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- EMDB-5927: Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Int... -

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Entry
Database: EMDB / ID: EMD-5927
TitleKinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle
Map data
SampleCoxsackievirus B3 complexed with CAR:
virus / Coxsackievirus and adenovirus receptor
Keywordscoxsackievirus b3 / cvb3 / CAR / cryoEM / A-particle
Function / homology
Function and homology information


AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport / cardiac muscle fiber development / negative regulation of cardiac muscle cell proliferation / cell-cell junction organization / connexin binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / intercalated disc / bicellular tight junction / actin cytoskeleton reorganization / acrosomal vesicle / mitochondrion organization / filopodium / cell adhesion molecule binding / PDZ domain binding / neutrophil chemotaxis / adherens junction / neuromuscular junction / beta-catenin binding / virus receptor activity / cell body / cell junction / cell-cell junction / growth cone / integrin binding / defense response to virus / regulation of immune response / heart development / leukocyte migration / basolateral plasma membrane / neuron projection / membrane raft / signaling receptor binding / integral component of plasma membrane / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin / Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin subtype 2
Coxsackievirus and adenovirus receptor
Biological speciesHuman coxsackievirus B3 (CVB3) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9 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.
Validation ReportSummary, Full report, XML, About validation report
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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  • Atomic modelsPDB-3j6l
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  • Atomic modelsPDB-3j6m
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  • Atomic modelsPDB-3j6n
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Structure viewerEM map:
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Downloads & links

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Map

FileDownload / File: emd_5927.map.gz / Format: CCP4 / Size: 206 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 381 pix.
= 476.25 Å		1.25 Å/pix.
x 381 pix.
= 476.25 Å		1.25 Å/pix.
x 381 pix.
= 476.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.67104959 - 5.68193388
Average (Standard dev.)-0.00000001 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-190-190-190
Dimensions381381381
Spacing381381381
CellA=B=C: 476.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z381381381
origin x/y/z0.0000.0000.000
length x/y/z476.250476.250476.250
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-190-190-190
NC/NR/NS381381381
D min/max/mean-4.6715.682-0.000

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Supplemental data

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Sample components

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Entire Coxsackievirus B3 complexed with CAR

EntireName: Coxsackievirus B3 complexed with CAR / Details: purified virus and receptor complex in solution / Number of components: 2 / Oligomeric State: icosahedral virus
MassExperimental: 7 MDa

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Component #1: virus, Human coxsackievirus B3

VirusName: Human coxsackievirus B3 / a.k.a: CVB3 / Class: VIRION
Details: Virus was incubated with excess CAR at 4 degrees C.
Enveloped: No / Empty: No / Isolate: STRAIN
MassExperimental: 7 MDa
SpeciesSpecies: Human coxsackievirus B3 (CVB3) / Strain: CVB3/28
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: VP1-4 / Diameter: 300 Å / T number (triangulation number): 1

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Component #2: protein, Coxsackievirus and adenovirus receptor

ProteinName: Coxsackievirus and adenovirus receptor / a.k.a: CAR / Recombinant expression: Yes
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)
External referencesUniProt: Coxsackievirus and adenovirus receptor

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/mL / Buffer solution: 50 mM MES, 100 mM NaCl / pH: 6
Support filmglow-discharged holey carbon Quantifoil electron microscopy grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 95 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Aug 1, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: CTFFIND3 / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1980 - 3660 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 96 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 9302 / Details: Particles were selected using EMAN.
3D reconstructionAlgorithm: Common Lines / Software: EMAN, AUTO3DEM / CTF correction: AUTO3DEM / Resolution: 9 Å / Resolution method: FSC 0.5, semi-independent

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Atomic model buiding

Modeling #1Software: Situs / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL
Details: The four available CAR structures were fit into the receptor density separately.
Input PDB model: 1F5W

1f5w


Chain ID: B
Modeling #2Software: Situs / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL
Details: The four available CAR structures were fit into the receptor density separately.
Input PDB model: 1KAC

1kac


Chain ID: B
Modeling #3Software: Situs / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL
Details: The four available CAR structures were fit into the receptor density separately.
Input PDB model: 3JZ7

3jz7


Chain ID: K
Modeling #4Software: Situs / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL
Details: The four available CAR structures were fit into the receptor density separately.
Input PDB model: 3MJ7

3mj7


Chain ID: S
Output model

3j6l

3j6m

3j6n

3j6o

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