2BPA | pdb_00002bpa

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/355137a0
  • Primary Citation 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,


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

Macromolecule Content 

  • Total Structure Weight: 73.09 kDa 
  • Atom Count: 5,298 
  • Modeled Residue Count: 642 
  • Deposited Residue Count: 643 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)B [auth 1]426Sinsheimervirus phiX174Mutation(s): 0 
UniProt
Find proteins for P03641 (Enterobacteria phage phiX174)
Explore P03641 
Go to UniProtKB:  P03641
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03641
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)C [auth 2]175Sinsheimervirus phiX174Mutation(s): 0 
UniProt
Find proteins for P03643 (Enterobacteria phage phiX174)
Explore P03643 
Go to UniProtKB:  P03643
Entity Groups
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UniProt GroupP03643
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)D [auth 3]37Sinsheimervirus phiX174Mutation(s): 0 
UniProt
Find proteins for P69592 (Enterobacteria phage phiX174)
Explore P69592 
Go to UniProtKB:  P69592
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69592
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*AP*C)-3')5N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 305.58α = 90
b = 360.78β = 92.89
c = 299.46γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations