- PDB-6ojn: Comparative Model of SGIV Major Coat Protein (MCP) Trimer Based o... -
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Basic information
Entry
Database: PDB / ID: 6ojn
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
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
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.
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