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- EMDB-3880: Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-3880
TitleCoxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
Map data
SampleCoxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1:
Coxsackievirus A24 / D1 and D2 domains of ICAM-1 / VP1 / VP2 / VP3 / Intercellular adhesion molecule 1
Function / homology
Function and homology information


T cell extravasation / response to gonadotropin / regulation of leukocyte mediated cytotoxicity / response to sulfur dioxide / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / establishment of Sertoli cell barrier / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell ...T cell extravasation / response to gonadotropin / regulation of leukocyte mediated cytotoxicity / response to sulfur dioxide / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / establishment of Sertoli cell barrier / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / acute inflammatory response to antigenic stimulus / cellular response to alkaloid / establishment of endothelial intestinal barrier / adhesion of symbiont to host / cellular response to nutrient levels / suppression by virus of host innate immune response / establishment of endothelial barrier / cellular response to interleukin-6 / cell adhesion mediated by integrin / positive regulation of leukocyte adhesion to vascular endothelial cell / response to ionizing radiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / response to copper ion / positive regulation of actin filament polymerization / Interleukin-10 signaling / immunological synapse / negative regulation of calcium ion transport / positive regulation of vasoconstriction / negative regulation of endothelial cell apoptotic process / cellular response to interleukin-1 / cell aging / ovarian follicle development / Integrin cell surface interactions / cellular response to leukemia inhibitory factor / response to insulin / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / response to amino acid / cellular response to dexamethasone stimulus / response to amphetamine / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / sensory perception of sound / RNA-protein covalent cross-linking / cellular response to glucose stimulus / receptor-mediated virion attachment to host cell / cellular response to amyloid-beta / positive regulation of GTPase activity / integral to membrane of host cell / pore formation by virus in membrane of host cell / virus receptor activity / Interferon gamma signaling / viral capsid / transmembrane signaling receptor activity / protein complex oligomerization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cytoplasmic vesicle membrane / positive regulation of nitric oxide biosynthetic process / cellular response to hypoxia / cellular response to tumor necrosis factor / positive regulation of peptidyl-tyrosine phosphorylation / interferon-gamma-mediated signaling pathway / endocytosis involved in viral entry into host cell / extracellular matrix organization / nucleoside-triphosphate phosphatase / integrin binding / regulation of immune response / signaling receptor activity / suppression by virus of host gene expression / ion channel activity / leukocyte migration / collagen-containing extracellular matrix / regulation of cell shape / response to ethanol / Interleukin-4 and Interleukin-13 signaling / positive regulation of ERK1 and ERK2 cascade / induction by virus of host autophagy / RNA-directed RNA polymerase / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / cell adhesion / viral entry into host cell / transcription, DNA-templated / external side of plasma membrane / virion attachment to host cell / membrane raft / host cell nucleus / response to drug / focal adhesion / cytokine-mediated signaling pathway / structural molecule activity / cell surface
Similarity search - Function
Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Poliovirus 3A protein-like / Poliovirus 3A protein like / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Picornavirus core protein 2A / Picornavirus 2B protein ...Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Poliovirus 3A protein-like / Poliovirus 3A protein like / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Picornavirus core protein 2A / Picornavirus 2B protein / Peptidase C3, 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 / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / Immunoglobulin / Immunoglobulin subtype / RdRp of positive ssRNA viruses catalytic domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Intercellular adhesion molecule 1 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A24 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHurdiss DL / Ranson NA
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus.
Authors: Jim Baggen / Daniel L Hurdiss / Georg Zocher / Nitesh Mistry / Richard W Roberts / Jasper J Slager / Hongbo Guo / Arno L W van Vliet / Maryam Wahedi / Kimberley Benschop / Erwin Duizer / ...Authors: Jim Baggen / Daniel L Hurdiss / Georg Zocher / Nitesh Mistry / Richard W Roberts / Jasper J Slager / Hongbo Guo / Arno L W van Vliet / Maryam Wahedi / Kimberley Benschop / Erwin Duizer / Cornelis A M de Haan / Erik de Vries / José M Casasnovas / Raoul J de Groot / Niklas Arnberg / Thilo Stehle / Neil A Ranson / Hendrik Jan Thibaut / Frank J M van Kuppeveld /
Abstract: Acute hemorrhagic conjunctivitis (AHC) is a painful, contagious eye disease, with millions of cases in the last decades. Coxsackievirus A24 (CV-A24) was not originally associated with human disease, ...Acute hemorrhagic conjunctivitis (AHC) is a painful, contagious eye disease, with millions of cases in the last decades. Coxsackievirus A24 (CV-A24) was not originally associated with human disease, but in 1970 a pathogenic "variant" (CV-A24v) emerged, which is now the main cause of AHC. Initially, this variant circulated only in Southeast Asia, but it later spread worldwide, accounting for numerous AHC outbreaks and two pandemics. While both CV-A24 variant and nonvariant strains still circulate in humans, only variant strains cause AHC for reasons that are yet unknown. Since receptors are important determinants of viral tropism, we set out to map the CV-A24 receptor repertoire and establish whether changes in receptor preference have led to the increased pathogenicity and rapid spread of CV-A24v. Here, we identify ICAM-1 as an essential receptor for both AHC-causing and non-AHC strains. We provide a high-resolution cryo-EM structure of a virus-ICAM-1 complex, which revealed critical ICAM-1-binding residues. These data could help identify a possible conserved mode of receptor engagement among ICAM-1-binding enteroviruses and rhinoviruses. Moreover, we identify a single capsid substitution that has been adopted by all pandemic CV-A24v strains and we reveal that this adaptation enhances the capacity of CV-A24v to bind sialic acid. Our data elucidate the CV-A24v receptor repertoire and point to a role of enhanced receptor engagement in the adaptation to the eye, possibly enabling pandemic spread.
History
DepositionSep 19, 2017-
Header (metadata) releaseSep 27, 2017-
Map releaseJan 10, 2018-
UpdateJan 17, 2018-
Current statusJan 17, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00701
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00701
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6eit
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6eit
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3880.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 464 pix.
= 494.206 Å
1.07 Å/pix.
x 464 pix.
= 494.206 Å
1.07 Å/pix.
x 464 pix.
= 494.206 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0651 Å
Density
Contour LevelBy AUTHOR: 0.00701 / Movie #1: 0.00701
Minimum - Maximum-0.1644654 - 0.17634246
Average (Standard dev.)0.0014059278 (±0.011912413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions464464464
Spacing464464464
CellA=B=C: 494.2064 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0650991379311.0650991379311.065099137931
M x/y/z464464464
origin x/y/z0.0000.0000.000
length x/y/z494.206494.206494.206
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS464464464
D min/max/mean-0.1640.1760.001

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Supplemental data

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Additional map: Coxsackievirus A24v in complex with the D1-D2 fragment...

Fileemd_3880_additional.map
AnnotationCoxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1 (unsharpened map).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1

EntireName: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1
Number of components: 7

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Component #1: protein, Coxsackievirus A24v in complex with the D1 and D2 domain...

ProteinName: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1
Recombinant expression: No
MassTheoretical: 8 MDa

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Component #2: protein, Coxsackievirus A24

ProteinName: Coxsackievirus A24 / Recombinant expression: No
SourceSpecies: Coxsackievirus A24

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Component #3: protein, D1 and D2 domains of ICAM-1

ProteinName: D1 and D2 domains of ICAM-1 / Recombinant expression: No
SourceSpecies: homo sapiens (human)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #4: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.378371 kDa
SourceSpecies: Coxsackievirus A24

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Component #5: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.817412 kDa
SourceSpecies: Coxsackievirus A24

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Component #6: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.637746 kDa
SourceSpecies: Coxsackievirus A24

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Component #7: protein, Intercellular adhesion molecule 1

ProteinName: Intercellular adhesion molecule 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.2976 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 10 mg/mL
Buffer solution: TBS buffer (Coxsackievirus A24v) Phosphate buffer (ICAM-1 D1-D2)
pH: 7.5
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 8 K / Humidity: 80 %
Details: On-grid binding of the receptor was performed by applying 3 microliters of ICAM-1 (9.85 mg/ml) to the pre-blotted, virus-containing grid, and leaving for 30 seconds before blotting and freezing.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2652

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (正20面体型対称) / Number of projections: 26311
3D reconstructionSoftware: RELION / CTF correction: gCTF / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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