1AL0

PROCAPSID OF BACTERIOPHAGE PHIX174


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Work: 0.316 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a viral procapsid with molecular scaffolding.

Dokland, T.McKenna, R.Ilag, L.L.Bowman, B.R.Incardona, N.L.Fane, B.A.Rossmann, M.G.

(1997) Nature 389: 308-313

  • DOI: 10.1038/38537

  • PubMed Abstract: 
  • The assembly of a macromolecular structure proceeds along an ordered morphogenetic pathway, and is accomplished by the switching of proteins between discrete conformations as they are added to the nascent assembly. Scaffolding proteins often play a c ...

    The assembly of a macromolecular structure proceeds along an ordered morphogenetic pathway, and is accomplished by the switching of proteins between discrete conformations as they are added to the nascent assembly. Scaffolding proteins often play a catalytic role in the assembly process, rather like molecular chaperones. Although macromolecular assembly processes are fundamental to all biological systems, they have been characterized most thoroughly in viral systems, such as the icosahedral Escherichia coli bacteriophage phiX174. The phiX174 virion contains the proteins F, G, H and J. During assembly, two scaffoldingproteins B and D are required for the formation of a 108S, 360-A-diameter procapsid from pentameric precursors containing the F, G and H proteins. The procapsid contains 240 copies of protein D, forming an external scaffold, and 60 copies each of the internal scaffolding protein B, the capsid protein F, and the spike protein G. Maturation involves packaging of DNA and J proteins and loss of protein B, producing a 132S intermediate. Subsequent removal of the external scaffold yields the mature virion. Both the F and G proteins have the eight-stranded antiparallel beta-sandwich motif common to many plant and animal viruses. Here we describe the structure of a procapsid-like particle at 3.5-A resolution, showing how the scaffolding proteins coordinate assembly of the virus by interactions with the F and G proteins, and showing that the F protein undergoes conformational changes during capsid maturation.


    Related Citations: 
    • DNA Packaging Intermediates of Bacteriophage Phi X174
      Ilag, L.L.,Olson, N.H.,Dokland, T.,Music, C.L.,Cheng, R.H.,Bowen, Z.,McKenna, R.,Rossmann, M.G.,Baker, T.S.,Incardona, N.L.
      (1995) Structure 3: 353
    • Biology of the Bacteriophage PhiX174
      Hayashi, M.,Aoyama, A.,Delwood, L.,Richardson, D.L.,Hayashi, M.N.
      (1988) The Bacteriophages (The Viruses) 2: 1
    • Nucleotide Sequence of Bacteriophage Phi X174 DNA
      Sanger, F.,Air, G.M.,Barrell, B.G.,Brown, N.L.,Coulson, A.R.,Fiddes, J.C.,Hutchison, C.A.,Slocombe, P.M.,Smith, M.
      (1977) Nature 265: 687
    • Analysis of the Single-Stranded DNA Bacteriophage Phi X174, Refined at a Resolution of 3.0 A
      McKenna, R.,Ilag, L.L.,Rossmann, M.G.
      (1994) J.Mol.Biol. 237: 517
    • 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, West Lafayette, Indiana 47907-1392, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SCAFFOLDING PROTEIN GPD
1, 2, 3, 4
152Enterobacteria phage phiX174Mutation(s): 0 
Gene Names: D
Find proteins for P69486 (Enterobacteria phage phiX174)
Go to UniProtKB:  P69486
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CAPSID PROTEIN GPF
F
426Enterobacteria phage phiX174Mutation(s): 0 
Gene Names: F
Find proteins for P03641 (Enterobacteria phage phiX174)
Go to UniProtKB:  P03641
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SPIKE PROTEIN GPG
G
175Enterobacteria phage phiX174Mutation(s): 0 
Gene Names: G
Find proteins for P03643 (Enterobacteria phage phiX174)
Go to UniProtKB:  P03643
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SCAFFOLDING PROTEIN GPB
B
120Enterobacteria phage phiX174Mutation(s): 0 
Gene Names: B
EC: 3.4.-.-
Find proteins for P03633 (Enterobacteria phage phiX174)
Go to UniProtKB:  P03633
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Work: 0.316 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 774.000α = 90.00
b = 774.000β = 90.00
c = 774.000γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance