3ZQO

Crystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 3)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural Basis for DNA Recognition and Loading Into a Viral Packaging Motor.

Buttner, C.R., Chechik, M., Ortiz-Lombardia, M., Smits, C., Ebong, I.O., Chechik, V., Jeschke, G., Dykeman, E., Benini, S., Robinson, C.V., Alonso, J.C., Antson, A.A.

(2012) Proc Natl Acad Sci U S A 109: 811

  • DOI: https://doi.org/10.1073/pnas.1110270109
  • Primary Citation of Related Structures:  
    3ZQM, 3ZQN, 3ZQO, 3ZQP, 3ZQQ

  • PubMed Abstract: 

    • Genome packaging into preformed viral procapsids is driven by powerful molecular motors. The small terminase protein is essential for the initial recognition of viral DNA and regulates the motor's ATPase and nuclease activities during DNA translocation. The crystal structure of a full-length small terminase protein from the Siphoviridae bacteriophage SF6, comprising the N-terminal DNA binding, the oligomerization core, and the C-terminal β-barrel domains, reveals a nine-subunit circular assembly in which the DNA-binding domains are arranged around the oligomerization core in a highly flexible manner ...

    Genome packaging into preformed viral procapsids is driven by powerful molecular motors. The small terminase protein is essential for the initial recognition of viral DNA and regulates the motor's ATPase and nuclease activities during DNA translocation. The crystal structure of a full-length small terminase protein from the Siphoviridae bacteriophage SF6, comprising the N-terminal DNA binding, the oligomerization core, and the C-terminal β-barrel domains, reveals a nine-subunit circular assembly in which the DNA-binding domains are arranged around the oligomerization core in a highly flexible manner. Mass spectrometry analysis and four further crystal structures show that, although the full-length protein exclusively forms nine-subunit assemblies, protein constructs missing the C-terminal β-barrel form both nine-subunit and ten-subunit assemblies, indicating the importance of the C terminus for defining the oligomeric state. The mechanism by which a ring-shaped small terminase oligomer binds viral DNA has not previously been elucidated. Here, we probed binding in vitro by using EPR and surface plasmon resonance experiments, which indicated that interaction with DNA is mediated exclusively by the DNA-binding domains and suggested a nucleosome-like model in which DNA binds around the outside of the protein oligomer.

    Organizational Affiliation: 

    York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TERMINASE SMALL SUBUNIT
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
72Bacillus phage SF6Mutation(s): 0 
Gene Names: 1
UniProt
Find proteins for P68928 (Bacillus phage SF6)
Explore P68928 
Go to UniProtKB:  P68928
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68928
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download Ideal Coordinates CCD File 
S [auth K],
T [auth R]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.202α = 90
b = 198.201β = 90.81
c = 59.202γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-01-18
    Changes: Other
  • Version 1.2: 2012-02-15
    Changes: Other