gpd prior to capsid assembly

Experimental Data Snapshot

  • Resolution: 3.31 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.280 

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This is version 1.3 of the entry. See complete history


Conformational switching by the scaffolding protein D directs the assembly of bacteriophage phiX174

Morais, M.C.Fisher, M.Kanamaru, S.Przybyla, L.Burgner, J.Fane, B.A.Rossmann, M.G.

(2004) Mol Cell 15: 991-997

  • DOI: https://doi.org/10.1016/j.molcel.2004.08.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The three-dimensional structure of bacteriophage phiX174 external scaffolding protein D, prior to its interaction with other structural proteins, has been determined to 3.3 angstroms by X-ray crystallography. The crystals belong to space group P4(1)2(1)2 with a dimer in the asymmetric unit that closely resembles asymmetric dimers observed in the phiX174 procapsid structure. Furthermore, application of the crystallographic 4(1) symmetry operation to one of these dimers generates a tetramer similar to the tetramer in the icosahedral asymmetric unit of the procapsid. These data suggest that both dimers and tetramers of the D protein are true morphogenetic intermediates and can form independently of other proteins involved in procapsid morphogenesis. The crystal structure of the D scaffolding protein thus represents the state of the polypeptide prior to procapsid assembly. Hence, comparison with the procapsid structure provides a rare opportunity to follow the conformational switching events necessary for the construction of complex macromolecular assemblies.

  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Scaffolding protein D
A, B
151Sinsheimervirus phiX174Mutation(s): 0 
Gene Names: D
Find proteins for P69486 (Enterobacteria phage phiX174)
Explore P69486 
Go to UniProtKB:  P69486
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69486
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.31 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.280 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.44α = 90
b = 106.44β = 90
c = 127.019γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Refinement description