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- EMDB-1114: The crystal structure of coxsackievirus A21 and its interaction w... -

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Basic information

Entry
Database: EMDB / ID: EMD-1114
TitleThe crystal structure of coxsackievirus A21 and its interaction with ICAM-1.
Map dataThis is an cryo-EM reconstructed map of human coxsackievirus A21 complex with 5 domain ICAM-1kilifi
Sample
  • Sample: Human Coxsackievirus A21 complex with ICAM-1KilifiFc
  • Virus: Human coxsackievirus A21
  • Protein or peptide: ICAM-1KilifiFc
Function / homology
Function and homology information


regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / : / establishment of endothelial barrier ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / : / establishment of endothelial barrier / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / leukocyte migration / Interleukin-10 signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to leukemia inhibitory factor / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cellular response to glucose stimulus / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cellular response to amyloid-beta / : / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / transmembrane signaling receptor activity / nucleoside-triphosphate phosphatase / integrin binding / virus receptor activity / signaling receptor activity / protein complex oligomerization / monoatomic ion channel activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / DNA replication / RNA helicase activity / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / induction by virus of host autophagy / RNA-directed RNA polymerase / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / cell surface / proteolysis / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like ...: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin subtype / Immunoglobulin / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Intercellular adhesion molecule 1 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus A21
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsXiao C / Bator-Kelly CM / Rieder E / Chipman PR / Craig A / Kuhn RJ / Wimmer E / Rossmann MG
CitationJournal: Structure / Year: 2005
Title: The crystal structure of coxsackievirus A21 and its interaction with ICAM-1.
Authors: Chuan Xiao / Carol M Bator-Kelly / Elizabeth Rieder / Paul R Chipman / Alister Craig / Richard J Kuhn / Eckard Wimmer / Michael G Rossmann /
Abstract: CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human ...CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 A resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 A resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1(Kilifi). The cryo-EM map was fitted with the crystal structures of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1.
History
DepositionMar 29, 2005-
Header (metadata) releaseMar 29, 2005-
Map releaseOct 4, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 83
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 83
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1z7z
  • Surface level: 83
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1z7z
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1114.gif

Downloads & links

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Map

FileDownload / File: emd_1114.map.gz / Format: CCP4 / Size: 190.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an cryo-EM reconstructed map of human coxsackievirus A21 complex with 5 domain ICAM-1kilifi
Voxel sizeX=Y=Z: 2 Å
Density
Contour Level1: 101.0 / Movie #1: 83
Minimum - Maximum-396.970000000000027 - 512.799999999999955
Average (Standard dev.)-1.83118 (±51.307299999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-185-185-185
Dimensions371371371
Spacing371371371
CellA=B=C: 742 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z371371371
origin x/y/z0.0000.0000.000
length x/y/z742.000742.000742.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-185-185-185
NX/NY/NZ371371371
MAP C/R/S213
start NC/NR/NS-185-185-185
NC/NR/NS371371371
D min/max/mean-396.970512.800-1.831

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Supplemental data

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Sample components

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Entire : Human Coxsackievirus A21 complex with ICAM-1KilifiFc

EntireName: Human Coxsackievirus A21 complex with ICAM-1KilifiFc
Components
  • Sample: Human Coxsackievirus A21 complex with ICAM-1KilifiFc
  • Virus: Human coxsackievirus A21
  • Protein or peptide: ICAM-1KilifiFc

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Supramolecule #1000: Human Coxsackievirus A21 complex with ICAM-1KilifiFc

SupramoleculeName: Human Coxsackievirus A21 complex with ICAM-1KilifiFc / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 11 MDa

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Supramolecule #1: Human coxsackievirus A21

SupramoleculeName: Human coxsackievirus A21 / type: virus / ID: 1 / Name.synonym: CVA21 / Details: CVA21 has 60 ICAM-1Kilifi bound on its surface / NCBI-ID: 12069 / Sci species name: Human coxsackievirus A21 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: CVA21
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 8 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 130 Å / T number (triangulation number): 1

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Macromolecule #1: ICAM-1KilifiFc

MacromoleculeName: ICAM-1KilifiFc / type: protein_or_peptide / ID: 1 / Name.synonym: ICAM-1Kilifi / Details: 60 ICAM-1Kilifi bound to one virus / Number of copies: 60 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Cell: COS7 / Location in cell: cell membrane
Molecular weightExperimental: 50 KDa
Recombinant expressionOrganism: COS7

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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

Concentration5.0 mg/mL
BufferpH: 7.2 / Details: 200mM NaCl, 10mM Tris-HCL
GridDetails: 200 mesh gold grid
VitrificationCryogen name: ETHANE / Chamber temperature: 80 K / Instrument: REICHERT-JUNG PLUNGER / Details: Vitrification instrument: Reichert plunger

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 45000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 80 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateMar 15, 2001
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 2.98 µm / Number real images: 33 / Average electron dose: 30 e/Å2 / Details: 7um step scanned and averaged to 14um / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: parallelized EMPFT, EM3DR / Number images used: 4704
Details7979 particles were manually boxed by using RobEM

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Atomic model buiding 1

Initial modelPDB ID:

1iam

SoftwareName: EMFIT
DetailsProtocol: Rigid Body. The domains were separately fitted.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Sumf
Output model

PDB-1z7z:
Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi

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