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

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Entry
Database: PDB / ID: 6eit
TitleCoxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
DescriptorVP1, Genome polyprotein, Intercellular adhesion molecule 1
KeywordsVIRUS / Enterovirus / Receptor / Complex / picornavirus
Specimen sourceHomo sapiens / human
Coxsackievirus A24 / virus
MethodElectron microscopy (3.9 Å resolution / Particle / Single particle)
AuthorsHurdiss, D.L. / Ranson, N.A.
CitationProc. Natl. Acad. Sci. U.S.A., 2018, 115, 397-402

Proc. Natl. Acad. Sci. U.S.A., 2018, 115, 397-402 Yorodumi Papers
Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus.
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: Polypeptide(L)VP1


Mass: 34378.371 Da / Num. of mol.: 1 / Source: (natural) Coxsackievirus A24 / virus / References: UniProt: G3C8J7
#2: Polypeptide(L)VP2


Mass: 29817.412 Da / Num. of mol.: 1 / Source: (natural) Coxsackievirus A24 / virus / References: UniProt: A0A088F913
#3: Polypeptide(L)VP3


Mass: 26637.746 Da / Num. of mol.: 1 / Source: (natural) Coxsackievirus A24 / virus / References: UniProt: Q0GYP7
#4: Polypeptide(L)Intercellular adhesion molecule 1 / ICAM-1 / Major group rhinovirus receptor


Mass: 9297.600 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / 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

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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 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1212089Coxsackievirus A24
239606homo sapiens
Source (recombinant)Organism: Cricetulus griseus
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 300 Å / 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 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) / Number of grids imaged: 1 / Number of real images: 2652

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Processing

EM softwareName: RELION / Version: 2 / Category: 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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