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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 dataCoxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
Sample
  • Complex: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1
    • Complex: Coxsackievirus A24
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
    • Complex: D1 and D2 domains of ICAM-1
      • Protein or peptide: Intercellular adhesion molecule 1
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 / RNA-protein covalent cross-linking / : ...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 / RNA-protein covalent cross-linking / : / : / 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 / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / cellular response to leukemia inhibitory factor / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cellular response to glucose stimulus / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / cellular response to amyloid-beta / viral capsid / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / nucleoside-triphosphate phosphatase / transmembrane signaling receptor activity / integrin binding / protein complex oligomerization / virus receptor activity / signaling receptor activity / monoatomic ion channel activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / 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 / symbiont entry into host cell / 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
Genome polyprotein / Capsid protein VP0 / Intercellular adhesion molecule 1 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A24 / homo sapiens (human) / 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

emd_3880.png

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)
AnnotationCoxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
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

Histogram

Histogram (log scale)

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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
Components
  • Complex: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1
    • Complex: Coxsackievirus A24
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
    • Complex: D1 and D2 domains of ICAM-1
      • Protein or peptide: Intercellular adhesion molecule 1

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Supramolecule #1: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1

SupramoleculeName: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 8 MDa

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Supramolecule #2: Coxsackievirus A24

SupramoleculeName: Coxsackievirus A24 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Coxsackievirus A24

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Supramolecule #3: D1 and D2 domains of ICAM-1

SupramoleculeName: D1 and D2 domains of ICAM-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A24
Molecular weightTheoretical: 34.378371 KDa
SequenceString: GIEETIDTVI TNALQLSQPK PQKQPTAQST PLTSGVNSQE VPALTAVETG ASGQAVPSDV IETRHVVNYK TRSESTLESF FGRSACVTI LEVENFNATT DADRKKQFTT WAITYTDTVQ LRRKLEFFTY SRFDLEMTFV ITERYYASNT GHARNQVYQL M YIPPGAPR ...String:
GIEETIDTVI TNALQLSQPK PQKQPTAQST PLTSGVNSQE VPALTAVETG ASGQAVPSDV IETRHVVNYK TRSESTLESF FGRSACVTI LEVENFNATT DADRKKQFTT WAITYTDTVQ LRRKLEFFTY SRFDLEMTFV ITERYYASNT GHARNQVYQL M YIPPGAPR PTAWDDYTWQ SSSNPSVFYT YGSAPPRMSI PYVGIANAYS HFYDGFARVP LKDETVDSGD TYYGLVTIND FG TLAVRVV NEYNPARITS KIRVYMKPKH VRCWCPRPPR AVPYRGEGVD FKQDSITPLT AVENINTF

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A24
Molecular weightTheoretical: 29.817412 KDa
SequenceString: SPNVEACGYS DRVRQITLGN STITTQEAAN AVVAYGEWPS YLDDKEANPI DAPTEPDVSS NRFYTLDSVQ WKSTSRGWWW KLPDALKDM GMFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YVMACNTEAK TSYVSYVNAN PGEKGGVFDN A YNPSAEAS ...String:
SPNVEACGYS DRVRQITLGN STITTQEAAN AVVAYGEWPS YLDDKEANPI DAPTEPDVSS NRFYTLDSVQ WKSTSRGWWW KLPDALKDM GMFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YVMACNTEAK TSYVSYVNAN PGEKGGVFDN A YNPSAEAS EGRKFAALDY LLGCGVLAGN AFVYPHQIIN LRTNNSATLV LPYVNSLAID CMAKHNNWGL VILPLCKLDY AP NSSTEIP ITVTIAPMFT EFNGLRNITV PATQ

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A24
Molecular weightTheoretical: 26.637746 KDa
SequenceString: GLPTMLTPGS SQFLTSDDFQ SPCALPNFDV TPPIHIPGEV FNMMELAEID SMIPMNSVTG KANTMEMYPI PLDDKGSATP IFSISLSPA SDKRLQYTML GEILNYYTHW TGSLRFTFLF CGSMMATGKI LLSYSPPGAK PPTTRKDAML GTHIIWDLGL Q SSCTMLAP ...String:
GLPTMLTPGS SQFLTSDDFQ SPCALPNFDV TPPIHIPGEV FNMMELAEID SMIPMNSVTG KANTMEMYPI PLDDKGSATP IFSISLSPA SDKRLQYTML GEILNYYTHW TGSLRFTFLF CGSMMATGKI LLSYSPPGAK PPTTRKDAML GTHIIWDLGL Q SSCTMLAP WISNTVYRRC IKDDFTEGGY ITCFYQTRIV VPSGTPTSMF MLAFVSACPD FSVRLLRDTN HISQRTLFAR AQ

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Macromolecule #4: Intercellular adhesion molecule 1

MacromoleculeName: Intercellular adhesion molecule 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.2976 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QTSVSPSKVI LPRGGSVLVT CSTSCDQPKL LGIETPLPKK ELLLPGNNRK VYELSNVQED SQPMCYSNCP DGQSTAKTFL TVYWT

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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

Concentration10 mg/mL
BufferpH: 7.5
Details: TBS buffer (Coxsackievirus A24v) Phosphate buffer (ICAM-1 D1-D2)
GridModel: Lacey grids coated in a 3 nm carbon film (Agar Scientific, UK)
Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 8 K / Instrument: LEICA EM GP
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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 2652 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: gCTF
Startup modelType of model: OTHER / Details: 300 Angstrom sphere generated in spider
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 26311
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6eit:
Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1

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