[English] 日本語

- EMDB-5927: Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Int... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-5927 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle | |||||||||
![]() | ||||||||||
![]() | Coxsackievirus B3 complexed with CAR: virus ![]() | |||||||||
![]() | coxsackievirus b3 / cvb3 / ![]() ![]() ![]() | |||||||||
Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Organtini LJ / Makhov AM / Conway JF / Hafenstein S / Carson SD | |||||||||
![]() | ![]() 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 | ![]() ![]() ![]() ![]() | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
-
Downloads & links
-
Download
Header (meta data in XML format) |
|
---|---|
![]() |
|
Archive directory |
-Related structure data
Related structure data | ![]() 3j6lCM ![]() 3j6mCM ![]() 3j6nCM ![]() 3j6oCM ![]() 5928C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar-shape strucutres |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire Coxsackievirus B3 complexed with CAR
Entire | Name: Coxsackievirus B3 complexed with CAR / Details: purified virus and receptor complex in solution / Number of components: 2 / 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. Enveloped: No / Empty: No / Isolate: STRAIN |
---|---|
Mass | Experimental: 7 MDa |
Species | Species: ![]() ![]() ![]() |
Source (natural) | Host Species: ![]() ![]() |
Shell #1 | Name of element: VP1-4 / Diameter: 300 Å / T number (triangulation number): 1 |
-Component #2: protein, Coxsackievirus and adenovirus receptor
Protein | Name: Coxsackievirus and adenovirus receptor / a.k.a: CAR![]() |
---|---|
Source | Species: ![]() ![]() |
Source (engineered) | Expression System: ![]() ![]() ![]() |
External references | UniProt: Coxsackievirus and adenovirus receptor |
-Experimental details
-
Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
---|---|
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
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
---|---|
![]() | Microscope: FEI TECNAI F20 / Date: Aug 1, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: CTFFIND3 / Cs: 2 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: GATAN LIQUID NITROGEN |
Camera | Detector: KODAK SO-163 FILM |
-Image acquisition
Image acquisition | Number of digital images: 96 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 µm |
---|
-
Image processing
![]() | Method: ![]() ![]() |
---|---|
3D reconstruction | Algorithm: Common Lines / Software: EMAN, AUTO3DEM / CTF correction: AUTO3DEM / Resolution: 9 Å / Resolution method: FSC 0.5, semi-independent |
-Atomic model buiding
Modeling #1 | Software: 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 Chain ID: B |
---|---|
Modeling #2 | Software: 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 Chain ID: B |
Modeling #3 | Software: 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 Chain ID: K |
Modeling #4 | Software: 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 Chain ID: S |
Output model |