3P9A | pdb_00003p9a

An atomic view of the nonameric small terminase subunit of Bacteriophage P22

• PDB DOI: https://doi.org/10.2210/pdb3P9A/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Lederbergvirus P22
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-17 Released: 2012-05-09 
• Deposition Author(s): Bhardwaj, A., Roy, A., Cingolani, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Small terminase couples viral DNA binding to genome-packaging ATPase activity.

Roy, A., Bhardwaj, A., Datta, P., Lander, G.C., Cingolani, G.

(2012) Structure 20: 1403-1413

• PubMed: 22771211 
• DOI: https://doi.org/10.1016/j.str.2012.05.014
• Primary Citation Related Structures: 
  3P9A


• PubMed Abstract: 
  

  Packaging of viral genomes into empty procapsids is powered by a large DNA-packaging motor. In most viruses, this machine is composed of a large (L) and a small (S) terminase subunit complexed with a dodecamer of portal protein. Here we describe the 1.75 Å crystal structure of the bacteriophage P22 S-terminase in a nonameric conformation. The structure presents a central channel ∼23 Å in diameter, sufficiently large to accommodate hydrated B-DNA. The last 23 residues of S-terminase are essential for binding to DNA and assembly to L-terminase. Upon binding to its own DNA, S-terminase functions as a specific activator of L-terminase ATPase activity. The DNA-dependent stimulation of ATPase activity thus rationalizes the exclusive specificity of genome-packaging motors for viral DNA in the crowd of host DNA, ensuring fidelity of packaging and avoiding wasteful ATP hydrolysis. This posits a model for DNA-dependent activation of genome-packaging motors of general interest in virology.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C9  (Explore in 3D)
Global Stoichiometry: Homo 9-mer - A9 

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

Macromolecule Content 

• Total Structure Weight: 168.08 kDa 
• Atom Count: 11,158 
• Modeled Residue Count: 1,202 
• Deposited Residue Count: 1,458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-packaging protein gp3	A, B, C, D, E, F, G, H, I	162	Lederbergvirus P22	Mutation(s): 0  Gene Names: 3
UniProt
Find proteins for P04893 (Salmonella phage P22) Explore P04893  Go to UniProtKB:  P04893

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.48	α = 90
b = 100.9	β = 93.73
c = 89.847	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Bhardwaj, A., Roy, A., Cingolani, G.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Database references
• Version 1.2: 2012-08-29
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references