[English] 日本語
Yorodumi
- EMDB-5927: Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Int... -

+
Open data


ID or keywords:

Loading...

-
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 / connexin binding ...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 / connexin binding / transepithelial transport / cell-cell junction organization / cardiac muscle cell development / heterophilic cell-cell adhesion / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / Cell surface interactions at the vascular wall / mitochondrion organization / filopodium / adherens junction / PDZ domain binding / neuromuscular junction / beta-catenin binding / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / cell junction / heart development / cell body / growth cone / virus receptor activity / actin cytoskeleton organization / 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j6l
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j6m
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j6n
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j6o
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6l
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6m
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6n
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6o
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5927.gif

Downloads & links

-
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

-
Supplemental data

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

-
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

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more