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

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Basic information

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 / homologyMajor capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / viral capsid / structural molecule activity / Major capsid protein
Function and homology information
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 support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM103832 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM079429 United States
CitationJournal: Structure / Year: 2019
Title: Segmentation and Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus.
Authors: Grigore Pintilie / Dong-Hua Chen / Bich Ngoc Tran / Joanita Jakana / Jinlu Wu / Choy Leong Hew / Wah Chiu /
Abstract: SGIV, or Singapore grouper iridovirus, is a large double-stranded DNA virus, reaching a diameter of 220 nm and packaging a genome of 140 kb. We present a 3D cryoelectron microscopy (cryo-EM) ...SGIV, or Singapore grouper iridovirus, is a large double-stranded DNA virus, reaching a diameter of 220 nm and packaging a genome of 140 kb. We present a 3D cryoelectron microscopy (cryo-EM) icosahedral reconstruction of SGIV determined at 8.6-Å resolution. It reveals several layers including a T = 247 icosahedral outer coat, anchor proteins, a lipid bilayer, and the encapsidated DNA. A new segmentation tool, iSeg, was applied to extract these layers from the reconstructed map. The outer coat was further segmented into major and minor capsid proteins. None of the proteins extracted by segmentation have known atomic structures. We generated models for the major coat protein using three comparative modeling tools, and evaluated each model using the cryo-EM map. Our analysis reveals a new architecture in the Iridoviridae family of viruses. It shares similarities with others in the same family, e.g., Chilo iridescent virus, but also shows new features of the major and minor capsid proteins.
History
DepositionApr 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9810 Å2
ΔGint-63 kcal/mol
Surface area51270 Å2

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Components

#1: Protein 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: all / 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 µm
Specimen holderCryogen: NITROGEN / Specimen holder 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 µm

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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

1m3y
PDB Unreleased entry


Accession code: 1M3Y / Source name: PDB / Type: experimental model

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