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- PDB-6gsi: Feline Calicivirus Strain F9 bound to a soluble ectodomain fragme... -

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Basic information

Entry
Database: PDB / ID: 6gsi
TitleFeline Calicivirus Strain F9 bound to a soluble ectodomain fragment of feline junctional adhesion molecule A - leading to assembly of a portal structure at a unique three-fold axis.
Components
  • Capsid proteinCapsid
  • Junctional adhesion molecule A
  • VP2
KeywordsVIRUS / Capsid / Calicivirus / Vesivirus / Vp1 / portal / Vp2 / junctional-adhesion molecule A
Function / homologyImmunoglobulin domain / Immunoglobulin-like domain / Ig-like domain profile. / Immunoglobulin V-set domain / Protein of unknown function (DUF743) / Calicivirus coat protein / Immunoglobulin-like domain superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin-like fold ...Immunoglobulin domain / Immunoglobulin-like domain / Ig-like domain profile. / Immunoglobulin V-set domain / Protein of unknown function (DUF743) / Calicivirus coat protein / Immunoglobulin-like domain superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin-like fold / Immunoglobulin V-set domain / Vesivirus VP2 / Calicivirus coat protein / Immunoglobulin subtype / Immunoglobulin subtype 2 / regulation of membrane permeability / establishment of endothelial intestinal barrier / T=3 icosahedral viral capsid / intestinal absorption / bicellular tight junction / virion / host cell cytoplasm / viral process / integral component of membrane / plasma membrane / Capsid protein / Protein VP2 / Junctional adhesion molecule A
Function and homology information
Specimen sourceFelis catus (domestic cat)
Feline calicivirus strain F9
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.75 Å resolution
AuthorsConley, M.J. / Bhella, D.
CitationJournal: Nature / Year: 2019
Title: Calicivirus VP2 forms a portal-like assembly following receptor engagement.
Authors: Michaela J Conley / Marion McElwee / Liyana Azmi / Mads Gabrielsen / Olwyn Byron / Ian G Goodfellow / David Bhella
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2018 / Release: Jan 16, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 16, 2019Structure modelrepositoryInitial release
1.1Jan 23, 2019Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Jan 30, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: VP2
J: VP2
K: VP2
L: VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,10516
Polyers430,94912
Non-polymers1564
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: VP2
J: VP2
K: VP2
L: VP2
hetero molecules

A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: VP2
J: VP2
K: VP2
L: VP2
hetero molecules

A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: VP2
J: VP2
K: VP2
L: VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,293,31548
Polyers1,292,84636
Non-polymers46912
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation2
Buried area (Å2)52450
ΔGint (kcal/M)-260
Surface area (Å2)130440
MethodPISA

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Components

#1: Protein/peptide
Capsid protein / Capsid / Coat protein / CP / VP1


Mass: 73346.664 Da / Num. of mol.: 4 / Source: (natural) Feline calicivirus strain F9 / References: UniProt: P27406
#2: Protein/peptide
Junctional adhesion molecule A / JAM-A / Junctional adhesion molecule 1 / JAM-1


Mass: 22180.650 Da / Num. of mol.: 4 / Fragment: UNP residues 29-230 / Source: (gene. exp.) Felis catus (domestic cat) / Gene: F11R, JAM1 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q2WGK2
#3: Protein/peptide
VP2 / Minor capsid protein


Mass: 12209.838 Da / Num. of mol.: 4 / Source: (natural) Feline calicivirus strain F9 / References: UniProt: P28711
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Formula: K / Potassium

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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
IDNameTypeDetailsEntity IDParent IDSource
1Feline calicivirus strain F9VIRUSVirus was propagated in Crandell Reese Feline Kidney cells1,2,30MULTIPLE SOURCES
2CapsidVIRUSIcosahedral Capsid11NATURAL
3feline junctional adhesion molecule ACOMPLEXSoluble ectodomain fragment comprising Ig-like domains D1 and D221RECOMBINANT
4VP2 - portal.COMPLEXPostulated to mediate endosome escape, this virion component is only present on the outer surface of the capsid following receptor engagement.31NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1211981Feline calicivirus strain F9
239685Felis catus (domestic cat)
3411981Feline calicivirus strain F9
Source (recombinant)Cell: CHO cells / Organism: Cricetulus griseus (Chinese hamster)
Details of virus
IDEntity assembly IDEmptyEnvelopedVirus isolateVirus type
11NONOSTRAINVIRION
22NONOSTRAINVIRION
Natural host
IDEntity assembly IDNcbi tax IDOrganism
119685Felis catus
229685Felis catus
Virus shell
IDNameEntity assembly IDDiameterTriangulation number (T number)
1Capsid14003
2Capsid24003
Buffer solutionDetails: Phosphate buffered saline / pH: 7.2
SpecimenConc.: 1 mg/ml
Details: Purified virions were incubated in the presence of purified ectodomain fragments.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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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 / Nominal magnification: 75000 / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 63 e/Å2
Details: Each micrograph was recorded as a movie of 50 individual fractions with a total dose of 63 e/angstrom squared
Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 1 / Number of real images: 13865

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
Image processingDetails: Images were motion-corrected using motioncor2 Defocus estimation was performed using GCTF
CTF correctionDetails: CTF correction was implemented through Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Autopicking in Relion / Number of particles selected: 129884
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 58510
Details: Origins and orientations were originally assigned by 3D auto refinement with full icosahedral symmetry. Random group assignment was carried through the focussed classification process and used to divide the data into two roughly even halves that had been initially refined independently.
Symmetry type: POINT

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