6OJN

Comparative Model of SGIV Major Coat Protein (MCP) Trimer Based on Cryo-EM Map

Summary for 6OJN

• Entry DOI: 10.2210/pdb6ojn/pdb
• EMDB information: 20091
• Descriptor: Major capsid protein (1 entity in total)
• Functional Keywords: icosahedral, trimers, outer coat, anchor proteins, zip proteins, viral protein
• Biological source: Singapore grouper iridovirus
• Total number of polymer chains: 3
• Total formula weight: 151719.42

Authors

Pintilie, G.,Chen, D.-H.,Tran, B.N.,Jakana, J.,Wu, J.,Hew, C.L.,Chiu, W. (deposition date: 2019-04-11, release date: 2019-06-12, Last modification date: 2024-03-20)

Primary citation

Pintilie, G.,Chen, D.H.,Tran, B.N.,Jakana, J.,Wu, J.,Hew, C.L.,Chiu, W.
Segmentation and Comparative Modeling in an 8.6- angstrom Cryo-EM Map of the Singapore Grouper Iridovirus.
Structure, 27:1561-, 2019

PubMed 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) 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.

PubMed: 31447288
DOI: 10.1016/j.str.2019.08.002

Experimental method

ELECTRON MICROSCOPY (8.6 Å)