Structure of the major structural protein D135 of Acidianus tailed spindle virus (ATSV)

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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Structural studies ofAcidianustailed spindle virus reveal a structural paradigm used in the assembly of spindle-shaped viruses.

Hochstein, R.Bollschweiler, D.Dharmavaram, S.Lintner, N.G.Plitzko, J.M.Bruinsma, R.Engelhardt, H.Young, M.J.Klug, W.S.Lawrence, C.M.

(2018) Proc Natl Acad Sci U S A 115: 2120-2125

  • DOI: https://doi.org/10.1073/pnas.1719180115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The spindle-shaped virion morphology is common among archaeal viruses, where it is a defining characteristic of many viral families. However, structural heterogeneity intrinsic to spindle-shaped viruses has seriously hindered efforts to elucidate the molecular architecture of these lemon-shaped capsids. We have utilized a combination of cryo-electron microscopy and X-ray crystallography to study Acidianus tailed spindle virus (ATSV). These studies reveal the architectural principles that underlie assembly of a spindle-shaped virus. Cryo-electron tomography shows a smooth transition from the spindle-shaped capsid into the tubular-shaped tail and allows low-resolution structural modeling of individual virions. Remarkably, higher-dose 2D micrographs reveal a helical surface lattice in the spindle-shaped capsid. Consistent with this, crystallographic studies of the major capsid protein reveal a decorated four-helix bundle that packs within the crystal to form a four-start helical assembly with structural similarity to the tube-shaped tail structure of ATSV and other tailed, spindle-shaped viruses. Combined, this suggests that the spindle-shaped morphology of the ATSV capsid is formed by a multistart helical assembly with a smoothly varying radius and allows construction of a pseudoatomic model for the lemon-shaped capsid that extends into a tubular tail. The potential advantages that this novel architecture conveys to the life cycle of spindle-shaped viruses, including a role in DNA ejection, are discussed.

  • Organizational Affiliation

    Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative major coat protein
A, B, C, D, E
142Acidianus tailed spindle virusMutation(s): 0 
Gene Names: ATSV_D135
Find proteins for A0A125SJ78 (Acidianus tailed spindle virus)
Explore A0A125SJ78 
Go to UniProtKB:  A0A125SJ78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125SJ78
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.78α = 90
b = 41.672β = 108.64
c = 97.69γ = 90
Software Package:
Software NamePurpose
Cootmodel building
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDEB-4W4596
National Science Foundation (NSF, United States)United StatesMCB-1413534
National Science Foundation (NSF, United States)United StatesMCB-0920312

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-02-14
    Changes: Database references
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence