Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C8  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.15 kDa 
• Atom Count: 2254 
• Modelled Residue Count: 253 
• Deposited Residue Count: 280 
• Unique protein chains: 1

4DYQ

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

• PDB DOI: 10.2210/pdb4DYQ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Shigella virus Sf6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-29 Released: 2012-10-17 
• Deposition Author(s): Zhao, H., Tang, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.202 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

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

• PubMed: 22858866 
• DOI: 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gene 1 protein	A, B	140	Shigella virus Sf6	Mutation(s): 0  Gene Names: gp1, 1
UniProt
Find proteins for Q716H4 (Shigella phage Sf6) Explore Q716H4  Go to UniProtKB:  Q716H4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 88.705	α = 90
b = 88.705	β = 90
c = 72.394	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-29 
• Released Date: 2012-10-17 
Deposition Author(s): Zhao, H., Tang, L.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description