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- PDB-6ojn: Comparative Model of SGIV Major Coat Protein (MCP) Trimer Based o... -

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Entry
Database: PDB / ID: 6ojn
TitleComparative Model of SGIV Major Coat Protein (MCP) Trimer Based on Cryo-EM Map
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / icosahedral / trimers / outer coat / anchor proteins / zip proteins
Function / homology
Function and homology information


viral capsid / structural molecule activity
Major capsid protein, C-terminal / Hexon coat protein, subdomain 4 / Group II dsDNA virus coat/capsid protein / Major capsid protein, N-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Major capsid protein N-terminus
Major capsid protein
Biological speciesSingapore grouper iridovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsPintilie, G. / Chen, D.-H. / Tran, B.N. / Jakana, J. / Wu, J. / Hew, C.L. / Chiu, W.
Funding supportUnited States , 2件
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteP41GM103832United States
National Institutes of Health/National Human Genome Research InstituteR01GM079429United States
CitationJournal: To be Published
Title: Segmentation and Comparative Modeling in a 8.6 Angstrom Cryo-EM Map of the 220 nm Diameter Singapore Grouper Iridovirus
Authors: Pintilie, G. / Chen, D.-H. / Tran, B.N. / Jakana, J. / Wu, J. / Hew, C.L. / Chiu, W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 11, 2019 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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Structure visualization

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)151,7193
Polymers151,7193
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9810 Å2
ΔGint-63 kcal/mol
Surface area51270 Å2

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Components

#1: Protein/peptide Major capsid protein


Mass: 50573.141 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Singapore grouper iridovirus / References: UniProt: Q5YFJ3

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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

ComponentName: Singapore grouper iridovirus / Type: VIRUS / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Singapore grouper iridovirus
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Epinephelus tauvina
Virus shellName: Outer coat / Diameter: 2200 nm / Triangulation number (T number): 247
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Blotted for 1 second before plunging.

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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 FIELDBright-field microscopy / Calibrated magnification: 63290 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µns
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansSampling size: 15 µns

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Processing

Software
NameVersionClassification
v1.9.1refinement
NAMDv2.12)refinement
EM software
IDNameCategory
4EMANCTF correction
9MPSAinitial Euler assignment
10MPSAfinal Euler assignment
12EMAN3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 19628
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9422 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Z-score of Cross Correlation scores
Atomic model buildingPDB-ID: 1M3Y

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