Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C12  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 842.91 kDa 
• Atom Count: 56559 
• Residue Count: 7020 
• Unique protein chains: 1

5JJ1

Structure of the Immature Procapsid Conformation of P22 Portal Protein

• DOI: 10.2210/pdb5JJ1/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Salmonella virus P22
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-22 Released: 2017-02-08 
• Deposition Author(s): Lokareddy, R.K., Cingolani, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.315 
• R-Value Work: 0.295 
• R-Value Observed: 0.295 

Literature

Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation.

Lokareddy, R.K., Sankhala, R.S., Roy, A., Afonine, P.V., Motwani, T., Teschke, C.M., Parent, K.N., Cingolani, G.

(2017) Nat Commun 8: 14310-14310

• PubMed: 28134243 
• DOI: 10.1038/ncomms14310
• Primary Citation of Related Structures:  
  5JJ1, 5JJ3


• PubMed Abstract: 
  

Tailed bacteriophages and herpesviruses assemble infectious particles via an empty precursor capsid (or 'procapsid') built by multiple copies of coat and scaffolding protein and by one dodecameric portal protein. Genome packaging triggers rearrangement of the coat protein and release of scaffolding protein, resulting in dramatic procapsid lattice expansion. Here, we provide structural evidence that the portal protein of the bacteriophage P22 exists in two distinct dodecameric conformations: an asymmetric assembly in the procapsid (PC-portal) that is competent for high affinity binding to the large terminase packaging protein, and a symmetric ring in the mature virion (MV-portal) that has negligible affinity for the packaging motor. Modelling studies indicate the structure of PC-portal is incompatible with DNA coaxially spooled around the portal vertex, suggesting that newly packaged DNA triggers the switch from PC- to MV-conformation. Thus, we propose the signal for termination of 'Headful Packaging' is a DNA-dependent symmetrization of portal protein.

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Organizational Affiliation: 

Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	A,  B,  C,  D,  E,  F,  G,  H,  I,  J,  K,  L	610	Salmonella virus P22	Mutation(s): 0  Gene Names: 1
Find proteins for P26744 (Salmonella phage P22) Explore P26744  Go to UniProtKB:  P26744

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.315 
• R-Value Work: 0.295 
• R-Value Observed: 0.295 
• Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 316.808	α = 90
b = 316.808	β = 90
c = 138.618	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-04-22 
• Released Date: 2017-02-08 
Deposition Author(s): Lokareddy, R.K., Cingolani, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM100888
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA56036

Revision History 

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2017-02-15
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence