6OJN

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Segmentation and Comparative Modeling in an 8.6- angstrom Cryo-EM Map of the Singapore Grouper Iridovirus.

Pintilie, G.Chen, D.H.Tran, B.N.Jakana, J.Wu, J.Hew, C.L.Chiu, W.

(2019) Structure 27: 1561

  • DOI: 10.1016/j.str.2019.08.002
  • Primary Citation of Related Structures:  
    6OJN

  • 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 ...

    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.


    Organizational Affiliation

    Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA; Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid proteinA, B, C463Singapore grouper iridovirusMutation(s): 0 
Gene Names: ORF072R
UniProt
Find proteins for Q5YFJ3 (Singapore grouper iridovirus)
Explore Q5YFJ3 
Go to UniProtKB:  Q5YFJ3
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP41GM103832
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM079429

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence