1GFF

THE ATOMIC STRUCTURE OF THE DEGRADED PROCAPSID PARTICLE OF THE BACTERIOPHAGE G4: INDUCED STRUCTURAL CHANGES IN THE PRESENCE OF CALCIUM IONS AND FUNCTIONAL IMPLICATIONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.352 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic structure of the degraded procapsid particle of the bacteriophage G4: induced structural changes in the presence of calcium ions and functional implications.

McKenna, R.Bowman, B.R.Ilag, L.L.Rossmann, M.G.Fane, B.A.

(1996) J Mol Biol 256: 736-750

  • DOI: 10.1006/jmbi.1996.0121
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bacteriophage G4 and phiX174 are members of the Microviridae family. The degree of similarity of the structural proteins ranges from 66% identity of the F protein to 40% identity of the G protein. The atomic structure of the phiX174 virion had previo ...

    Bacteriophage G4 and phiX174 are members of the Microviridae family. The degree of similarity of the structural proteins ranges from 66% identity of the F protein to 40% identity of the G protein. The atomic structure of the phiX174 virion had previously been determined by X-ray crystallography. Bacteriophage G4 procapsids, consisting of the structural proteins F, G, D, B, H, and small traces of J but no DNA, were set up for crystallization. However, the resultant crystals were of degraded procapsid particles, which had lost the assembly scaffolding proteins D and B, resulting in particles that resembled empty virions. The structure of the degraded G4 procapsid has been determined to 3.0 angstrom resolution. The particles crystallized in the hexagonal space group P6(3)22 with unit cell dimensions a=b=414.2(5) angstrom and c=263.0(3) angstrom. The diffraction data were collected at the Cornell High Energy Synchrotron Source (CHESS) on film and image plates using oscillation photography. Packing considerations indicated there were two particles per unit cell. A self-rotation function confirmed that the particles were positioned on 32 point group special positions in the unit cell. Initial phases were calculated to 6 angstrom resolution, based on the known phiX174 virion model. Phase information was then extended in steps to 3.0 angstrom resolution by molecular replacement electron density modification and particle envelope generation. The resulting electron density map was readily interpretable in terms of the F and G polypeptides, as occur in the mature capsid of phiX174. In a few regions of the electron density map there were inconsistencies between the density and the published amino acid sequence. Redetermining the amino acid sequence confirmed that the density was correct. The r.m.s. deviation between the Calpha backbone of the mature capsid of phiX174 and the degraded G4 procapsid was 0.36 angstrom for the F protein and 1.38 angstrom for the G protein. This is consistent with the greater conservation of the F protein compared to the G protein sequences among members of the Microviridae family. Functionally important features between phiX174 and G4 had greater conservation. Calcium ions (Ca2+) were shown to bind to G4 at a general site located near the icosahedral 3-fold axis on the F protein capsid, equivalent to sites found previously in phiX174. Binding of Ca2+ also caused the ordering of the conserved region of the DNA binding protein J, which was present in the degraded procapsid particle in the absence of DNA.


    Related Citations: 
    • Analysis of the Single-Stranded DNA Bacteriophage PhiX174 Refined at a Resolution of 3.0 Angstroms
      McKenna, R., Ilag, L.L., Rossmann, M.G.
      (1994) J Mol Biol 237: 517
    • Atomic Structure of Single-Stranded DNA Bacteriophage PhiX174 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
    • Biology of the Bacteriophage PhiX174
      Hayashi, M., Aoyama, A., Delwood, L., Richardson, D.L., Hayashi, M.N.
      (1988) The Bacteriophages (the Viruses) 2: 1
    • Comparative DNA Sequence Analysis of the G4 and PhiX174 Genomes
      Godson, G.N., Fiddles, J.C., Barrell, B.G., Sanger, F.
      (1978) The Single-stranded Dna Phages --: 51

    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ1426Escherichia phage G4Mutation(s): 0 
Gene Names: F
Find proteins for P03642 (Escherichia phage G4)
Explore P03642 
Go to UniProtKB:  P03642
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ2177Escherichia phage G4Mutation(s): 0 
Gene Names: G
Find proteins for P03644 (Escherichia phage G4)
Explore P03644 
Go to UniProtKB:  P03644
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ325Escherichia phage G4Mutation(s): 0 
Gene Names: J
Find proteins for P03652 (Escherichia phage G4)
Explore P03652 
Go to UniProtKB:  P03652
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.352 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 414.2α = 90
b = 414.2β = 90
c = 263γ = 120

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1995-11-06 
  • Released Date: 1996-04-03 
  • Deposition Author(s): Rossmann, M.G.

Revision History 

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance