Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 240-mer - A180B60 

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

Macromolecule Content

• Total Structure Weight: 150.15 kDa 
• Atom Count: 5945 
• Modelled Residue Count: 757 
• Deposited Residue Count: 1384 
• Unique protein chains: 2

3NB3

The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components

• PDB DOI: 10.2210/pdb3NB3/pdb
• EM Map EMD-5201:EMDBEMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2010-06-02 Released: 2011-02-16 
• Deposition Author(s): Zhao, H., Sequeira, R.D., Galeva, N.A., Tang, L.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 19.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion.

Zhao, H., Sequeira, R.D., Galeva, N.A., Tang, L.

(2011) Virology 409: 319-327

• PubMed: 21071053 
• DOI: 10.1016/j.virol.2010.10.030
• Primary Citation of Related Structures:  
  3NB3


• PubMed Abstract: 
  

Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J.Mol.Biol. 339, 379-394, Fig. 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. This density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of this density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state.

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Organizational Affiliation: 

Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein A	A, B, C	346	Escherichia coli K-12	Mutation(s): 0  Gene Names: ompA, con, tolG, tut, b0957, JW0940
UniProt
Find proteins for P0A910 (Escherichia coli (strain K12)) Explore P0A910  Go to UniProtKB:  P0A910

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein C	D	346	Escherichia coli K-12	Mutation(s): 0  Gene Names: ompC, meoA, par, b2215, JW2203
UniProt
Find proteins for P06996 (Escherichia coli (strain K12)) Explore P06996  Go to UniProtKB:  P06996

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 19.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-02 
• Released Date: 2011-02-16 
Deposition Author(s): Zhao, H., Sequeira, R.D., Galeva, N.A., Tang, L.

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-25
  Changes: Atomic model, Other, Source and taxonomy
• Version 1.3: 2016-11-09
  Changes: Other
• Version 1.4: 2019-12-11
  Changes: Data collection, Structure summary