5FS4

Bacteriophage AP205 coat protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Ap205 Coat Protein Reveals Circular Permutation in Ssrna Bacteriophages.

Shishovs, M.Rumnieks, J.Diebolder, C.Jaudzems, K.Andreas, L.B.Stanek, J.Kazaks, A.Kotelovica, S.Akopjana, I.Pintacuda, G.Koning, R.I.Tars, K.

(2016) J.Mol.Biol. 428: 4267

  • DOI: 10.1016/j.jmb.2016.08.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an una ...

    AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions.


    Organizational Affiliation

    Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AP205 BACTERIOPHAGE COAT PROTEIN
A, B
133Acinetobacter phage AP205Mutation(s): 2 
Find proteins for Q9AZ42 (Acinetobacter phage AP205)
Go to UniProtKB:  Q9AZ42
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 28.600α = 90.00
b = 114.930β = 98.14
c = 42.800γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
BUCCANEERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-12-29 
  • Released Date: 2016-09-21 
  • Deposition Author(s): Shishovs, M., Tars, K.

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation