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Yorodumi- PDB-6ojn: Comparative Model of SGIV Major Coat Protein (MCP) Trimer Based o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ojn | |||||||||
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Title | Comparative Model of SGIV Major Coat Protein (MCP) Trimer Based on Cryo-EM Map | |||||||||
Components | Major capsid protein | |||||||||
Keywords | VIRAL PROTEIN / icosahedral / trimers / outer coat / anchor proteins / zip proteins | |||||||||
Function / homology | Major 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 species | Singapore grouper iridovirus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.6 Å | |||||||||
Authors | Pintilie, G. / Chen, D.-H. / Tran, B.N. / Jakana, J. / Wu, J. / Hew, C.L. / Chiu, W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ojn.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ojn.ent.gz | 187.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ojn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ojn_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ojn_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6ojn_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 6ojn_validation.cif.gz | 80.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/6ojn ftp://data.pdbj.org/pub/pdb/validation_reports/oj/6ojn | HTTPS FTP |
-Related structure data
Related structure data | 20091MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Singapore grouper iridovirus / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Singapore grouper iridovirus |
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Epinephelus tauvina |
Virus shell | Name: Outer coat / Diameter: 2200 nm / Triangulation number (T number): 247 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Blotted for 1 second before plunging. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 63290 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Sampling size: 15 µm |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||
Particle selection | Num. of particles selected: 19628 | |||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||
3D reconstruction | Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9422 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Z-score of Cross Correlation scores | |||||||||||||||
Atomic model building | PDB-ID: 1M3Y 1m3y Accession code: 1M3Y / Source name: PDB / Type: experimental model |