1CJD

THE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR TO HUMAN ADENOVIRUS HEXON

• PDB DOI: https://doi.org/10.2210/pdb1CJD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Enterobacteria phage PRD1
• Expression System: Salmonella enterica subsp. enterica serovar Typhimurium
• Mutation(s): No 


• Deposited: 1999-04-12 Released: 1999-09-20 
• Deposition Author(s): Benson, S.D., Bamford, J.K.H., Bamford, D.H., Burnett, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.205 (Depositor) 
• R-Value Work: 
  0.178 (Depositor), 0.200 (DCC) 

Literature

Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures.

Benson, S.D., Bamford, J.K., Bamford, D.H., Burnett, R.M.

(1999) Cell 98: 825-833

• PubMed: 10499799 
• DOI: https://doi.org/10.1016/s0092-8674(00)81516-0
• Primary Citation of Related Structures:  
  1CJD


• PubMed Abstract: 
  

  The unusual bacteriophage PRD1 features a membrane beneath its icosahedral protein coat. The crystal structure of the major coat protein, P3, at 1.85 A resolution reveals a molecule with three interlocking subunits, each with two eight-stranded viral jelly rolls normal to the viral capsid, and putative membrane-interacting regions. Surprisingly, the P3 molecule closely resembles hexon, the equivalent protein in human adenovirus. Both viruses also have similar overall architecture, with identical capsid lattices and attachment proteins at their vertices. Although these two dsDNA viruses infect hosts from very different kingdoms, their striking similarities, from major coat protein through capsid architecture, strongly suggest their evolutionary relationship.

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Organizational Affiliation: 

The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 130.04 kDa 
• Atom Count: 8,975 
• Modelled Residue Count: 1,108 
• Deposited Residue Count: 1,182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (MAJOR CAPSID PROTEIN (P3))	A, B, C	394	Enterobacteria phage PRD1	Mutation(s): 0
UniProt
Find proteins for P22535 (Enterobacteria phage PRD1) Explore P22535  Go to UniProtKB:  P22535

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.205 (Depositor) 
• R-Value Work:  0.178 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.956	α = 90
b = 121.296	β = 90
c = 126.387	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-09-20 
Deposition Author(s): Benson, S.D., Bamford, J.K.H., Bamford, D.H., Burnett, R.M.

Revision History  

• Version 1.0: 1999-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-27
  Changes: Database references
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references