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

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Basic information

Entry
Database: EMDB / ID: EMD-5927
TitleKinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle
Map dataReconstruction of CVB3 complexed with CAR
Sample
  • Sample: Coxsackievirus B3 complexed with CAR
  • Virus: Human coxsackievirus B3
  • Protein or peptide: 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 / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / 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 / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport / connexin binding / cell-cell junction organization / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / Cell surface interactions at the vascular wall / filopodium / PDZ domain binding / adherens junction / mitochondrion organization / neuromuscular junction / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell junction / cell-cell junction / heart development / virus receptor activity / actin cytoskeleton organization / cell body / growth cone / basolateral plasma membrane / defense response to virus / neuron projection / membrane raft / signaling receptor binding / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Human 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
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  • Atomic models: PDB-3j6m
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  • Atomic models: PDB-3j6n
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  • Atomic models: PDB-3j6o
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6l
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5927.gif

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)
AnnotationReconstruction of CVB3 complexed with CAR
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
Components
  • Sample: Coxsackievirus B3 complexed with CAR
  • Virus: Human coxsackievirus B3
  • Protein or peptide: Coxsackievirus and adenovirus receptor

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Supramolecule #1000: Coxsackievirus B3 complexed with CAR

SupramoleculeName: Coxsackievirus B3 complexed with CAR / type: sample / ID: 1000 / Details: purified virus and receptor complex in solution / Oligomeric state: icosahedral virus / Number unique components: 2
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.
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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Macromolecule #1: Coxsackievirus and adenovirus receptor

MacromoleculeName: Coxsackievirus and adenovirus receptor / type: protein_or_peptide / ID: 1 / Name.synonym: CAR / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Coxsackievirus and adenovirus receptor

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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
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: 96 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.66 µm / Nominal defocus min: 1.98 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected using EMAN.
CTF correctionDetails: AUTO3DEM
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: EMAN, AUTO3DEM / Number images used: 9302

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Atomic model buiding 1

Initial modelPDB ID:

1f5w


Chain - Chain ID: B
SoftwareName: Situs
DetailsThe four available CAR structures were fit into the receptor density separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-3j6l:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6m:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6n:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6o:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

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Atomic model buiding 2

Initial modelPDB ID:

1kac


Chain - Chain ID: B
SoftwareName: Situs
DetailsThe four available CAR structures were fit into the receptor density separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-3j6l:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6m:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6n:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6o:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

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Atomic model buiding 3

Initial modelPDB ID:

3jz7


Chain - Chain ID: K
SoftwareName: Situs
DetailsThe four available CAR structures were fit into the receptor density separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-3j6l:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6m:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6n:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6o:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

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Atomic model buiding 4

Initial modelPDB ID:

3mj7


Chain - Chain ID: S
SoftwareName: Situs
DetailsThe four available CAR structures were fit into the receptor density separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-3j6l:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6m:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6n:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

PDB-3j6o:
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle

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