1RB8

The phiX174 DNA binding protein J in two different capsid environments.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The phiX174 Protein J Mediates DNA Packaging and Viral Attachment to Host Cells.

Bernal, R.A.Hafenstein, S.Esmeralda, R.Fane, B.A.Rossmann, M.G.

(2004) J.Mol.Biol. 337: 1109-1122

  • DOI: 10.1016/j.jmb.2004.02.033

  • PubMed Abstract: 
  • Packaging of viral genomes into their respective capsids requires partial neutralization of the highly negatively charged RNA or DNA. Many viruses, including the Microviridae bacteriophages phiX174, G4, and alpha3, have solved this problem by coding ...

    Packaging of viral genomes into their respective capsids requires partial neutralization of the highly negatively charged RNA or DNA. Many viruses, including the Microviridae bacteriophages phiX174, G4, and alpha3, have solved this problem by coding for a highly positively charged nucleic acid-binding protein that is packaged along with the genome. The phiX174 DNA-binding protein, J, is 13 amino acid residues longer than the alpha3 and G4 J proteins by virtue of an additional nucleic acid-binding domain at the amino terminus. Chimeric phiX174 particles containing the smaller DNA-binding protein cannot be generated due to procapsid instability during DNA packaging. However, chimeric alpha3 and G4 phages, containing the phiX174 DNA-binding protein in place of the endogenous J protein, assemble and are infectious, but are less dense than the respective wild-type species. In addition, host cell attachment and native gel migration assays indicate surface variations of these viruses that are controlled by the nature of the J protein. The structure of alpha3 packaged with phiX174 J protein was determined to 3.5A resolution and compared with the previously determined structures of phiX174 and alpha3. The structures of the capsid and spike proteins in the chimeric particle remain unchanged within experimental error when compared to the wild-type alpha3 virion proteins. The amino-terminal region of the phiX174 J protein, which is missing from wild-type alpha3 virions, is mostly disordered in the alpha3 chimera. The differences observed between solution properties of wild-type phiX174, wild-type alpha3, and alpha3 chimera, including their ability to attach to host cells, correlates with the degree of order in the amino-terminal domain of the J protein. When ordered, this domain binds to the interior of the viral capsid and, thus, might control the flexibility of the capsid. In addition, the properties of the phiX174 J protein in the chimera and the results of mutational analyses suggest that an evolutionary correlation may exist between the size of the J protein and the stoichiometry of the DNA pilot protein H, required in the initial stages of infection. Hence, the function of the J protein is to facilitate DNA packaging, as well as to mediate surface properties such as cell attachment and infection.


    Related Citations: 
    • Structural Studies of Bacteriophage Alpha3 Assembly
      Bernal, R.A.,Hafenstein, S.,Olson, N.H.,Bowman, V.D.,Chipman, P.R.,Baker, T.S.,Fane, B.A.,Rossmann, M.G.
      (2003) J.Mol.Biol. 325: 11
    • The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174.
      Dokland, T.,Bernal, R.A.,Burch, A.,Pletnev, S.,Fane, B.A.,Rossmann, M.G.
      (1999) J.Mol.Biol. 288: 595
    • Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications.
      McKenna, R.,Xia, D.,Willingmann, P.,Ilag, L.L.,Krishnaswamy, S.,Rossmann, M.G.,Olson, N.H.,Baker, T.S.,Incardona, N.L.
      (1992) Nature 355: 137


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
F
431Enterobacteria phage alpha3Gene Names: F
Find proteins for P08767 (Enterobacteria phage alpha3)
Go to UniProtKB:  P08767
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Major spike protein
G
187Enterobacteria phage alpha3Gene Names: G
Find proteins for P31281 (Enterobacteria phage alpha3)
Go to UniProtKB:  P31281
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small core protein
J
37Enterobacteria phage phiX174Gene Names: J
Find proteins for P69592 (Enterobacteria phage phiX174)
Go to UniProtKB:  P69592
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*AP*AP*A)-3')X4N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DC
Query on DC

Download SDF File 
Download CCD File 
X
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.234 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 295.143α = 90.00
b = 295.143β = 90.00
c = 678.235γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SnBphasing
ENVELOPEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation