3C6A

Crystal Structure of the RB49 gp17 nuclease domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.

Sun, S.Kondabagil, K.Draper, B.Alam, T.I.Bowman, V.D.Zhang, Z.Hegde, S.Fokine, A.Rossmann, M.G.Rao, V.B.

(2008) Cell 135: 1251-1262

  • DOI: 10.1016/j.cell.2008.11.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which p ...

    Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which provides energy for compacting DNA, and a C-terminal nuclease domain, which terminates packaging. We show that another function of the C-terminal domain is to translocate the genome into the procapsid. The two domains are in close contact in the crystal structure, representing a "tensed state." A cryo-electron microscopy reconstruction of the T4 procapsid complexed with gp17 shows that the packaging motor is a pentamer and that the domains within each monomer are spatially separated, representing a "relaxed state." These structures suggest a mechanism, supported by mutational and other data, in which electrostatic forces drive the DNA packaging by alternating between tensed and relaxed states. Similar mechanisms may occur in other molecular motors.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Terminase large subunit
A
232Enterobacteria phage RB49Mutation(s): 0 
Gene Names: 17
Find proteins for Q9T1C3 (Enterobacteria phage RB49)
Go to UniProtKB:  Q9T1C3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.134 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 52.568α = 90.00
b = 125.163β = 90.00
c = 37.218γ = 90.00
Software Package:
Software NamePurpose
SOLOMONphasing
SHELXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SHELXL-97refinement
DENZOdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description