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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 / homologyInterleukin-4 and Interleukin-13 signaling / Intercellular adhesion molecule / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Immunoglobulin-like fold / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain ...Interleukin-4 and Interleukin-13 signaling / Intercellular adhesion molecule / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Immunoglobulin-like fold / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Poliovirus core protein 3a, soluble domain / Immunoglobulin subtype / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Interferon gamma signaling / Immunoglobulin-like domain superfamily / Intercellular adhesion molecule, N-terminal / picornavirus capsid protein / Intercellular adhesion molecule (ICAM), N-terminal domain / Interleukin-10 signaling / 3C cysteine protease (picornain 3C) / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Picornavirus coat protein (VP4) / Picornavirus core protein 2A / RNA dependent RNA polymerase / RNA helicase / Picornavirus 2B protein / Integrin cell surface interactions / regulation of leukocyte mediated cytotoxicity / positive regulation of cellular extravasation / T cell extravasation / response to sulfur dioxide / T cell antigen processing and presentation / response to gonadotropin / establishment of Sertoli cell barrier / 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 / negative regulation of calcium ion transport / 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 / T=pseudo3 icosahedral viral capsid / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / positive regulation of vasoconstriction / suppression by virus of host RIG-I activity / picornain 3C / cellular response to interleukin-1 / cellular response to leukemia inhibitory factor / negative regulation of endothelial cell apoptotic process / ovarian follicle development / response to insulin / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / cellular response to dexamethasone stimulus / cell aging / response to amino acid / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to glucose stimulus / sensory perception of sound / positive regulation of GTPase activity / extracellular matrix / RNA helicase activity / pore formation by virus in membrane of host cell / integral to membrane of host cell / transmembrane signaling receptor activity / virus receptor activity / nucleoside-triphosphatase / viral capsid / integrin binding / signaling receptor activity / cellular response to tumor necrosis factor / cellular response to hypoxia / interferon-gamma-mediated signaling pathway
Function and homology information
Specimen sourceHomo sapiens (human)
Coxsackievirus A24
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsHurdiss, D.L. / Ranson, N.A.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 19, 2017 / Release: Jan 10, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 10, 2018Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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
Polyers100,1314
Non-polymers00
Water0
1
1: VP1
2: VP2
3: VP3
4: Intercellular adhesion molecule 1
x 60


Theoretical massNumber of molelcules
Total (without water)6,007,868240
Polyers6,007,868240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation59
Buried area (Å2)11340
ΔGint (kcal/M)-49
Surface area (Å2)41720
MethodUCSF CHIMERA 1.10.1_b40427.

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Components

#1: Protein/peptide VP1


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


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


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


Mass: 9297.600 Da / Num. of mol.: 1 / 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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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-1COMPLEX1, 2, 3, 40MULTIPLE SOURCES
2Coxsackievirus A24COMPLEX1, 2, 31NATURAL
3D1 and D2 domains of ICAM-1COMPLEX41RECOMBINANT
Molecular weightValue: 8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1212089Coxsackievirus A24
239606homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 300 nm / Triangulation number (T number): 3
Buffer solutionDetails: TBS buffer (Coxsackievirus A24v) Phosphate buffer (ICAM-1 D1-D2)
pH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400
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 kelvins
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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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) / Number of grids imaged: 1 / Number 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
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 26311 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL

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