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

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Entry
Database: EMDB / ID: 3880
TitleCoxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
Map dataCoxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
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/homologypositive regulation of cellular extravasation / regulation of leukocyte mediated cytotoxicity / response to sulfur dioxide / T cell antigen processing and presentation / response to gonadotropin / establishment of Sertoli cell barrier / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal ...positive regulation of cellular extravasation / regulation of leukocyte mediated cytotoxicity / response to sulfur dioxide / T cell antigen processing and presentation / response to gonadotropin / establishment of Sertoli cell barrier / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / regulation of ruffle assembly / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / establishment of endothelial intestinal barrier / positive regulation of leukocyte adhesion to vascular endothelial cell / acute inflammatory response to antigenic stimulus / adhesion of symbiont to host / cellular response to nutrient levels / establishment of endothelial barrier / cellular response to interleukin-6 / cell adhesion mediated by integrin / receptor-mediated virion attachment to host cell / response to ionizing radiation / cellular response to alkaloid / leukocyte cell-cell adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / immunological synapse / response to copper ion / response to amphetamine / positive regulation of actin filament polymerization / Interleukin-10 signaling / T=pseudo3 icosahedral viral capsid / Poliovirus 3A protein-like / Peptidase C3, picornavirus core protein 2A / Poliovirus 3A protein like / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Picornavirus coat protein VP4 / picornain 2A / Picornavirus 2B protein / Picornavirus core protein 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / negative regulation of calcium ion transport / positive regulation of vasoconstriction / cellular response to interleukin-1 / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / response to insulin / negative regulation of endothelial cell apoptotic process / ovarian follicle development / cellular response to leukemia inhibitory factor / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / Peptidase C3A/C3B, picornaviral / Picornavirus coat protein (VP4) / Integrin cell surface interactions / cell aging / cellular response to glucose stimulus / cellular response to dexamethasone stimulus / Picornavirus capsid / 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 / 3C cysteine protease (picornain 3C) / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Picornavirus/Calicivirus coat protein / RNA-directed RNA polymerase, C-terminal domain / sensory perception of sound / response to amino acid / RNA dependent RNA polymerase / positive regulation of GTPase activity / transmembrane signaling receptor activity / RNA helicase activity / pore formation by virus in membrane of host cell / integral to membrane of host cell / virus receptor activity / viral capsid / nucleoside-triphosphatase / cellular response to tumor necrosis factor / Interferon gamma signaling / cellular response to hypoxia / picornavirus capsid protein / interferon-gamma-mediated signaling pathway / go:0004872: / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / extracellular matrix organization / RNA-directed RNA polymerase / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / suppression by virus of host gene expression / regulation of immune response / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / positive regulation of peptidyl-tyrosine phosphorylation / extracellular matrix
Function and homology information
SourceCoxsackievirus A24 / virus
Homo sapiens / / human
MethodCryo EM / single particle (icosahedral) reconstruction / 3.9 Å resolution
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 / 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.
Validation ReportPDB-ID: 6eit

SummaryFull reportAbout validation report
DateDeposition: Sep 19, 2017 / Header (metadata) release: Sep 27, 2017 / Map release: Jan 10, 2018 / Last update: Jan 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00701
  • Imaged by UCSF CHIMERA
  • Download
  • 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 models: PDB-6eit
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_3880.map.gz (map file in CCP4 format, 399590 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.0651 Å
Density
Contour Level:0.00701 (by author), 0.00701 (movie #1):
Minimum - Maximum-0.1644654 - 0.17634246
Average (Standard dev.)0.0014059278 (0.011912413)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions464464464
Origin000
Limit463463463
Spacing464464464
CellA=B=C: 494.2064 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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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
MassTheoretical: 8 MDa

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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
SourceSpecies:

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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
Source (engineered)Expression System: Cricetulus griseus

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Component #4: protein, VP1

ProteinName: VP1 / Recombinant expression: No
MassTheoretical: 34.378371 kDa
SourceSpecies: Coxsackievirus A24

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Component #5: protein, VP2

ProteinName: VP2 / Recombinant expression: No
MassTheoretical: 29.817412 kDa
SourceSpecies: Coxsackievirus A24

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Component #6: protein, VP3

ProteinName: VP3 / 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 / Recombinant expression: No
MassTheoretical: 9.2976 kDa
SourceSpecies:
Source (engineered)Expression System: Homo sapiens

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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: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 2652

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 26311
3D reconstructionSoftware: RELION / CTF correction: gCTF / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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