6WQ2

Cryo-EM of the S. islandicus filamentous virus, SIFV

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments.

Wang, F., Baquero, D.P., Beltran, L.C., Su, Z., Osinski, T., Zheng, W., Prangishvili, D., Krupovic, M., Egelman, E.H.

(2020) Proc Natl Acad Sci U S A 117: 19643-19652

  • DOI: 10.1073/pnas.2011125117
  • Primary Citation of Related Structures:  
    6WQ0, 6WQ2

  • PubMed Abstract: 

    • Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2 ...

    Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and Sulfolobus islandicus filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908; mart.krupovic@pasteur.fr egelman@virginia.edu.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Structural protein MCP2167Sulfolobus islandicus filamentous virusMutation(s): 0 
UniProt
Find proteins for Q914J5 (Sulfolobus islandicus filamentous virus (isolate Iceland/Hveragerdi))
Explore Q914J5 
Go to UniProtKB:  Q914J5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ914J5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Structural protein MCP1204Sulfolobus islandicus filamentous virusMutation(s): 0 
UniProt
Find proteins for Q914J4 (Sulfolobus islandicus filamentous virus (isolate Iceland/Hveragerdi))
Explore Q914J4 
Go to UniProtKB:  Q914J4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ914J4
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
A-DNAA [auth 1]225Sulfolobus islandicus filamentous virus
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
A-DNAB [auth 2]223Sulfolobus islandicus filamentous virus
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM122510

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Database references