4BTP

Structure of the capsid protein P1 of the bacteriophage phi8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Plate Tectonics of Virus Shell Assembly and Reorganization in Phage Phi8, a Distant Relative of Mammalian Reoviruses

El Omari, K.Sutton, G.Ravantti, J.J.Zhang, H.Walter, T.S.Grimes, J.M.Bamford, D.H.Stuart, D.I.Mancini, E.J.

(2013) Structure 21: 1374

  • DOI: 10.1016/j.str.2013.06.017
  • Primary Citation of Related Structures:  
    4BX4, 4BTP

  • PubMed Abstract: 
  • The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein multiplicity (120 copies) to form their closed capsids. We have determined the atomic structure of the capsid protein (P1) from the dsRNA cystovirus Φ8 ...

    The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein multiplicity (120 copies) to form their closed capsids. We have determined the atomic structure of the capsid protein (P1) from the dsRNA cystovirus Φ8. In the crystal P1 forms pentamers, very similar in shape to facets of empty procapsids, suggesting an unexpected assembly pathway that proceeds via a pentameric intermediate. Unlike the elongated proteins used by dsRNA mammalian reoviruses, P1 has a compact trapezoid-like shape and a distinct arrangement in the shell, with two near-identical conformers in nonequivalent structural environments. Nevertheless, structural similarity with the analogous protein from the mammalian viruses suggests a common ancestor. The unusual shape of the molecule may facilitate dramatic capsid expansion during phage maturation, allowing P1 to switch interaction interfaces to provide capsid plasticity.


    Organizational Affiliation

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
p1
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
792Pseudomonas phage phi8Mutation(s): 2 
Gene Names: 1
Find proteins for Q9MC13 (Pseudomonas phage phi8)
Explore Q9MC13 
Go to UniProtKB:  Q9MC13
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 314.351α = 90
b = 314.35β = 90
c = 527.943γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL2Mapphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 2.0: 2018-10-03
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary