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

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Basic information

Entry
Database: PDB / ID: 6eit
TitleCoxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
Components
  • Intercellular adhesion molecule 1
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / Enterovirus / Receptor / Complex / picornavirus
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 / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion / leukocyte migration / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / 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 / ribonucleoside triphosphate phosphatase activity / cellular response to leukemia inhibitory factor / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / cellular response to glucose stimulus / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / integrin binding / cellular response to amyloid-beta / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / viral capsid / transmembrane signaling receptor activity / signaling receptor activity / host cell / nucleoside-triphosphate phosphatase / : / channel activity / virus receptor activity / monoatomic ion transmembrane transport / Interleukin-4 and Interleukin-13 signaling / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / RNA helicase activity / cell adhesion / membrane raft / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / external side of plasma membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / cell surface / proteolysis / extracellular space / RNA binding / extracellular exosome / zinc ion binding / ATP binding / membrane / 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 / Jelly Rolls - #20 / 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 / Jelly Rolls - #20 / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Immunoglobulin-like domain superfamily / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Intercellular adhesion molecule 1 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Coxsackievirus A24
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHurdiss, D.L. / Ranson, N.A.
Funding support Netherlands, Germany, United Kingdom, 3items
OrganizationGrant numberCountry
Netherlands Organization for Scientific ResearchNWO-VICI-91812628 Netherlands
German Research FoundationSFB685 Germany
Wellcome Trust102572/B/13/Z United Kingdom
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, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Assembly

Deposited unit
1: VP1
2: VP2
3: VP3
4: Intercellular adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)100,1314
Polymers100,1314
Non-polymers00
Water00
1
1: VP1
2: VP2
3: VP3
4: Intercellular adhesion molecule 1
x 60


Theoretical massNumber of molelcules
Total (without water)6,007,868240
Polymers6,007,868240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area11340 Å2
ΔGint-49 kcal/mol
Surface area41720 Å2
MethodUCSF CHIMERA
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP1


Mass: 34378.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / Cell line: Normal human conjunctival (NHC) cells / References: UniProt: G3C8J7, UniProt: V9VEF3*PLUS
#2: Protein VP2


Mass: 29817.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / Cell line: Normal human conjunctival (NHC) cells / References: UniProt: A0A088F913, UniProt: V9VEF3*PLUS
#3: Protein VP3


Mass: 26637.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / Cell line: Normal human conjunctival (NHC) cells / References: UniProt: Q0GYP7, UniProt: V9VEF3*PLUS
#4: Protein Intercellular adhesion molecule 1 / ICAM-1 / Major group rhinovirus receptor


Mass: 9297.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM1 / Cell line (production host): CHO Lec3.2.8.1 cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05362
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1COMPLEXall0MULTIPLE SOURCES
2Coxsackievirus A24COMPLEX#1-#31NATURAL
3D1 and D2 domains of ICAM-1COMPLEX#41RECOMBINANT
Molecular weightValue: 8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Coxsackievirus A2412089
23homo sapiens (human)9606
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.5
Details: TBS buffer (Coxsackievirus A24v) Phosphate buffer (ICAM-1 D1-D2)
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
Grid type: Lacey grids coated in a 3 nm carbon film (Agar Scientific, UK)
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 8 K
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2652

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Processing

EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionDetails: gCTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26311 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL

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