High resolution crystal structure of terminase small subunit gp1 of the bacterial virus sf6

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Structural and Functional Studies of the Phage Sf6 Terminase Small Subunit Reveal a DNA-Spooling Device Facilitated by Structural Plasticity.

Zhao, H.Kamau, Y.N.Christensen, T.E.Tang, L.

(2012) J Mol Biol 423: 413-426

  • DOI: https://doi.org/10.1016/j.jmb.2012.07.016
  • Primary Citation of Related Structures:  
    4DYC, 4DYQ, 4DYR, 4DZJ, 4DZP

  • PubMed Abstract: 

    In many DNA viruses, genome packaging is initiated by the small subunit of the packaging terminase, which specifically binds to the packaging signal on viral DNA and directs assembly of the terminase holoenzyme. We have experimentally mapped the DNA-interacting region on Shigella virus Sf6 terminase small subunit gp1, which occupies extended surface areas encircling the gp1 octamer, indicating that DNA wraps around gp1 through extensive contacts. High-resolution structures reveal large-scale motions of the gp1 DNA-binding domain mediated by the curved helix formed by residues 54-81 and an intermolecular salt bridge formed by residues Arg67 and Glu73, indicating remarkable structural plasticity underlying multivalent, pleomorphic gp1:DNA interactions. These results provide spatial restraints for protein:DNA interactions, which enable construction of a three-dimensional pseudo-atomic model for a DNA-packaging initiation complex assembled from the terminase small subunit and the packaging region on viral DNA. Our results suggest that gp1 functions as a DNA-spooling device, which may transform DNA into a specific architecture appropriate for interaction with and cleavage by the terminase large subunit prior to DNA translocation into viral procapsid. This may represent a common mechanism for the initiation step of DNA packaging in tailed double-stranded DNA bacterial viruses.

  • Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gene 1 protein
A, B
140Lederbergvirus Sf6Mutation(s): 0 
Gene Names: gp1
Find proteins for Q716H4 (Shigella phage Sf6)
Explore Q716H4 
Go to UniProtKB:  Q716H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ716H4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.705α = 90
b = 88.705β = 90
c = 72.394γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description