Biological Assembly 1  

 3D View: Structure

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 180-mer - A60B60C60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 73.09 kDa 
• Atom Count: 5298 
• Modelled Residue Count: 642 
• Deposited Residue Count: 643 
• Unique protein chains: 3
• Unique nucleic acid chains: 1

2BPA

ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS

• DOI: 10.2210/pdb2BPA/pdb
• NDB: PDV002

• Classification: Virus/DNA
• Organism(s): Escherichia virus phiX174
• Expression System: Escherichia coli C
• Mutation(s): No 


• Deposited: 1991-12-03 Released: 1991-12-03 
• Deposition Author(s): McKenna, R., Xia, D., Willingmann, P., Ilag, L.L., Krishnaswamy, S., Rossmann, M.G., Olson, N.H., Baker, T.S., Incardona, N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Observed: 0.209 

Literature

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: 137-143

• PubMed: 1370343 
• DOI: 10.1038/355137a0
• Primary Citation of Related Structures:  
  2BPA


• PubMed Abstract: 
  

The mechanism of DNA ejection, viral assembly and evolution are related to the structure of bacteriophage phi X174. The F protein forms a T = 1 capsid whose major folding motif is the eight-stranded antiparallel beta barrel found in many other icosahedral viruses. Groups of 5 G proteins form 12 dominating spikes that enclose a hydrophilic channel containing some diffuse electron density. Each G protein is a tight beta barrel with its strands running radially outwards and with a topology similar to that of the F protein. The 12 'pilot' H proteins per virion may be partially located in the putative ion channel. The small, basic J protein is associated with the DNA and is situated in an interior cleft of the F protein. Tentatively, there are three regions of partially ordered DNA structure,

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Related Citations: 

• Structure Determination of the Bacteriophage PhiX174
  McKenna, R., Xia, D., Willingmann, P., Ilag, L.L., Rossmann, M.G.
  (1992) Acta Crystallogr B 48: 499

• Analysis of the Single-Stranded DNA Bacteriophage PhiX174 Refined at a Resolution of 3.0 A
  McKenna, R., Ilag, L.L., Rossmann, M.G.
  (1994) J Mol Biol 237: 517

• Preliminary Investigation of the Phage PhiX174
  Willingmann, P., Krishnaswamy, S., McKenna, R., Smith, T.J., Olson, N.H., Rossmann, M.G., Stow, P.L., Incardona, N.L.
  (1990) J Mol Biol 212: 345

• Biology of the Bacteriophage PhiX174
  Hayashi, M., Adyama, A., Delwood, L., Richardson, D.L., Hayashi, M.N.
  (1988) The Bacteriophages (the Viruses) 2: 1

• Nucleoside Sequence of Bacteriophage PhiX174 DNA
  Sanger, F., Air, G.M., Barrell, B.G., Brown, N.L., Coulson, A.R., Fiddes, J.C., Hutchinson, C.A., Slocombe, P.M., Smith, M.
  (1977) Nature 265: 687

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)	B [auth 1]	426	Escherichia virus phiX174	Mutation(s): 0
Find proteins for P03641 (Enterobacteria phage phiX174) Explore P03641  Go to UniProtKB:  P03641

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)	C [auth 2]	175	Escherichia virus phiX174	Mutation(s): 0
Find proteins for P03643 (Enterobacteria phage phiX174) Explore P03643  Go to UniProtKB:  P03643

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)	D [auth 3]	37	Escherichia virus phiX174	Mutation(s): 0
Find proteins for P69592 (Enterobacteria phage phiX174) Explore P69592  Go to UniProtKB:  P69592

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*AP*C)-3')	A	5	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 305.58	α = 90
b = 360.78	β = 92.89
c = 299.46	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1991-12-03 
• Released Date: 1991-12-03 
Deposition Author(s): McKenna, R., Xia, D., Willingmann, P., Ilag, L.L., Krishnaswamy, S., Rossmann, M.G., Olson, N.H., Baker, T.S., Incardona, N.L.

Revision History  

• Version 1.0: 1991-12-03
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance