3HEF

Crystal structure of the bacteriophage Sf6 terminase small subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine

Zhao, H.Finch, C.J.Sequeira, R.D.Johnson, B.A.Johnson, J.E.Casjens, S.R.Tang, L.

(2010) Proc.Natl.Acad.Sci.USA 107: 1971-1976

  • DOI: 10.1073/pnas.0908569107

  • PubMed Abstract: 
  • In herpesviruses and many bacterial viruses, genome-packaging is a precisely mediated process fulfilled by a virally encoded molecular machine called terminase that consists of two protein components: A DNA-recognition component that defines the spec ...

    In herpesviruses and many bacterial viruses, genome-packaging is a precisely mediated process fulfilled by a virally encoded molecular machine called terminase that consists of two protein components: A DNA-recognition component that defines the specificity for packaged DNA, and a catalytic component that provides energy for the packaging reaction by hydrolyzing ATP. The terminase docks onto the portal protein complex embedded in a single vertex of a preformed viral protein shell called procapsid, and pumps the viral DNA into the procapsid through a conduit formed by the portal. Here we report the 1.65 A resolution structure of the DNA-recognition component gp1 of the Shigella bacteriophage Sf6 genome-packaging machine. The structure reveals a ring-like octamer formed by interweaved protein monomers with a highly extended fold, embracing a tunnel through which DNA may be translocated. The N-terminal DNA-binding domains form the peripheral appendages surrounding the octamer. The central domain contributes to oligomerization through interactions of bundled helices. The C-terminal domain forms a barrel with parallel beta-strands. The structure reveals a common scheme for oligomerization of terminase DNA-recognition components, and provides insights into the role of gp1 in formation of the packaging-competent terminase complex and assembly of the terminase with the portal, in which ring-like protein oligomers stack together to form a continuous channel for viral DNA translocation.


    Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gene 1 protein
A, B
143Shigella phage Sf6Mutation(s): 0 
Gene Names: 1
Find proteins for Q716H4 (Shigella phage Sf6)
Go to UniProtKB:  Q716H4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.224 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.858α = 90.00
b = 88.858β = 90.00
c = 72.631γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
SCALEPACKdata scaling
DENZOdata reduction
SOLVEphasing
CNSrefinement
Blu-Icedata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-05-08 
  • Released Date: 2010-02-09 
  • Deposition Author(s): Zhao, H., Tang, L.

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description