4BTP | pdb_00004btp

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 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4BTP

This is version 2.1 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: https://doi.org/10.1016/j.str.2013.06.017
  • Primary Citation Related Structures: 
    4BTP, 4BX4

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 869.99 kDa 
  • Atom Count: 57,630 
  • Modeled Residue Count: 7,490 
  • Deposited Residue Count: 7,920 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
p1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
792Pseudomonas phage phi8Mutation(s): 2 
UniProt
Find proteins for Q9MC13 (Pseudomonas phage phi8)
Explore Q9MC13 
Go to UniProtKB:  Q9MC13
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9MC13
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
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

View Full Validation Report



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
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references, Other