Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 33644.24 
• Atom Count: 2125 
• Residue Count: 302 
• Unique protein chains: 1

1TX9

gpd prior to capsid assembly

• DOI: 10.2210/pdb1TX9/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Enterobacteria phage phiX174
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2004-06-24 Released: 2005-04-26 
• Deposition Author(s): Morais, M.C., Fisher, M., Kanamaru, K., Fane, B.A., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.310 
• R-Value Work: 0.271 

Literature

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

• PubMed: 15383287 
• DOI: 10.1016/j.molcel.2004.08.023


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Scaffolding protein D	A, B	151	Enterobacteria phage phiX174	Mutation(s): 0  Gene Names: D
Find proteins for P69486 (Enterobacteria phage phiX174) Go to UniProtKB:  P69486

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.310 
• R-Value Work: 0.271 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 106.440	α = 90.00
b = 106.440	β = 90.00
c = 127.019	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
AMoRE	phasing
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-24 
• Released Date: 2005-04-26 
• Deposition Author(s): Morais, M.C., Fisher, M., Kanamaru, K., Fane, B.A., Rossmann, M.G.

Revision History 

• Version 1.0: 2005-04-26
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance