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Title: Segmentation and Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus

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. Here, 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.

Authors:
 [1];  [2];  [3];  [4];  [3];  [3];  [5]
+ Show Author Affiliations
  1. Stanford Univ., Stanford, CA (United States). Dept. of Bioengineering, and of Microbiology and Immunology
  2. Stanford Univ., Stanford, CA (United States). Dept. of Structural Biology
  3. National Univ. of Singapore (Singapore). Dept. of Biological Sciences
  4. Baylor College of Medicine, Houston, TX (United States). Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology
  5. Stanford Univ., Stanford, CA (United States). Dept. of Bioengineering, and of Microbiology and Immunology; Stanford Univ., Stanford, CA (United States). Div. of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Lab.
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1575122
Grant/Contract Number:  
AC02-76SF00515; R01GM079429; P41GM103832; P41-GM103311
Resource Type:
Accepted Manuscript
Journal Name:
Structure
Additional Journal Information:
Journal Volume: 27; Journal Issue: 10; Journal ID: ISSN 0969-2126
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; iridovirus; cryo-EM; icosahedral segmentation; comparative modeling; trisymmetron; pentasymmetron; jelly-roll domain; anchor protein; lipid membrane

Citation Formats

Pintilie, Grigore, Chen, Dong -Hua, Tran, Bich Ngoc, Jakana, Joanita, Wu, Jinlu, Hew, Choy Leong, and Chiu, Wah. Segmentation and Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus. United States: N. p., 2019. Web. doi:10.1016/j.str.2019.08.002.
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Pintilie, Grigore, Chen, Dong -Hua, Tran, Bich Ngoc, Jakana, Joanita, Wu, Jinlu, Hew, Choy Leong, & Chiu, Wah. Segmentation and Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus. United States. https://doi.org/10.1016/j.str.2019.08.002
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Pintilie, Grigore, Chen, Dong -Hua, Tran, Bich Ngoc, Jakana, Joanita, Wu, Jinlu, Hew, Choy Leong, and Chiu, Wah. Thu . "Segmentation and Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus". United States. https://doi.org/10.1016/j.str.2019.08.002. https://www.osti.gov/servlets/purl/1575122.
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@article{osti_1575122,
title = {Segmentation and Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus},
author = {Pintilie, Grigore and Chen, Dong -Hua and Tran, Bich Ngoc and Jakana, Joanita and Wu, Jinlu and Hew, Choy Leong and Chiu, Wah},
abstractNote = {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. Here, 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.},
doi = {10.1016/j.str.2019.08.002},
journal = {Structure},
number = 10,
volume = 27,
place = {United States},
year = {Thu Aug 22 00:00:00 EDT 2019},
month = {Thu Aug 22 00:00:00 EDT 2019}
}
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https://doi.org/10.1016/j.str.2019.08.002
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Works referenced in this record:

Insights into assembly from structural analysis of bacteriophage PRD1
journal, November 2004

  • Abrescia, Nicola G. A.; Cockburn, Joseph J. B.; Grimes, Jonathan M.
  • Nature, Vol. 432, Issue 7013
  • DOI: 10.1038/nature03056

Real-space refinement in PHENIX for cryo-EM and crystallography
journal, May 2018

  • Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
  • DOI: 10.1107/S2059798318006551

Iridovirus and Microsporidian Linked to Honey Bee Colony Decline
journal, October 2010

DNA packaging orders the membrane of bacteriophage PRD1.
journal, December 1995

Physical Principles in the Construction of Regular Viruses
journal, January 1962

Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus
journal, January 2011

  • Chen, D. -H.; Baker, M. L.; Hryc, C. F.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1015739108

iTRAQ analysis of Singapore grouper iridovirus infection in a grouper embryonic cell line
journal, November 2008

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

A new iridovirus isolated from soft-shelled turtle
journal, September 1999

Ranaviruses (family Iridoviridae): emerging cold-blooded killers
journal, March 2002

Comparative Protein Structure Modeling Using MODELLER
journal, November 2007

  • Eswar, Narayanan; Webb, Ben; Marti-Renom, Marc A.
  • Current Protocols in Protein Science, Vol. 50, Issue 1
  • DOI: 10.1002/0471140864.ps0209s50

The Isolation and Properties of Viruses from rana Pipiens: Their Possible Relationship to the Renal Adenocarcinoma of the Leopard Frog*
journal, August 1965

VMD: Visual molecular dynamics
journal, February 1996

Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America
journal, November 2003

Evidence for Multiple Recent Host Species Shifts among the Ranaviruses (Family Iridoviridae)
journal, December 2009

  • Jancovich, James K.; Bremont, Michel; Touchman, Jeffrey W.
  • Journal of Virology, Vol. 84, Issue 6
  • DOI: 10.1128/JVI.01991-09

Protein structure prediction on the Web: a case study using the Phyre server
journal, February 2009

  • Kelley, Lawrence A.; Sternberg, Michael J. E.
  • Nature Protocols, Vol. 4, Issue 3
  • DOI: 10.1038/nprot.2009.2

Local Average Intensity-Based Method for Identifying Spherical Particles in Electron Micrographs
journal, August 2000

  • Kivioja, Teemu; Ravantti, Janne; Verkhovsky, Anatoly
  • Journal of Structural Biology, Vol. 131, Issue 2
  • DOI: 10.1006/jsbi.2000.4279

EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions
journal, December 1999

  • Ludtke, Steven J.; Baldwin, Philip R.; Chiu, Wah
  • Journal of Structural Biology, Vol. 128, Issue 1
  • DOI: 10.1006/jsbi.1999.4174

The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus
journal, October 2002

  • Nandhagopal, N.; Simpson, A. A.; Gurnon, J. R.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 23
  • DOI: 10.1073/pnas.232580699

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage
journal, February 2016

  • Pintilie, Grigore; Chen, Dong-Hua; Haase-Pettingell, Cameron A.
  • Biophysical Journal, Vol. 110, Issue 4
  • DOI: 10.1016/j.bpj.2015.11.3522

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
journal, June 2010

  • Pintilie, Grigore D.; Zhang, Junjie; Goddard, Thomas D.
  • Journal of Structural Biology, Vol. 170, Issue 3
  • DOI: 10.1016/j.jsb.2010.03.007

Collapse of Amphibian Communities Due to an Introduced Ranavirus
journal, November 2014

  • Price, Stephen J.; Garner, Trenton W. J.; Nichols, Richard A.
  • Current Biology, Vol. 24, Issue 21
  • DOI: 10.1016/j.cub.2014.09.028

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae
journal, April 2015

  • Reteno, Dorine Gaëlle; Benamar, Samia; Khalil, Jacques Bou
  • Journal of Virology, Vol. 89, Issue 13
  • DOI: 10.1128/JVI.00115-15

Functional Genomics Analysis of Singapore Grouper Iridovirus: Complete Sequence Determination and Proteomic Analysis
journal, November 2004

Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting
journal, April 2006

  • Topf, Maya; Baker, Matthew L.; Marti-Renom, Marc A.
  • Journal of Molecular Biology, Vol. 357, Issue 5
  • DOI: 10.1016/j.jmb.2006.01.062

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
journal, May 2008

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
journal, October 2009

The versatile β-barrel membrane protein
journal, August 2003

Lipidomic study of intracellular Singapore grouper iridovirus
journal, April 2010

The Capsid Proteins of a Large, Icosahedral dsDNA Virus
journal, January 2009

Estimating contrast transfer function and associated parameters by constrained non-linear optimization
journal, March 2009

The I-TASSER Suite: protein structure and function prediction
journal, December 2014

  • Yang, Jianyi; Yan, Renxiang; Roy, Ambrish
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3213

Three-dimensional structure and function of the Paramecium bursaria chlorella virus capsid
journal, August 2011

  • Zhang, X.; Xiang, Y.; Dunigan, D. D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 36
  • DOI: 10.1073/pnas.1107847108
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