5J37

Crystal structure of 60-mer BFDV Capsid Protein in complex with single stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the assembly and regulation of distinct viral capsid complexes.

Sarker, S.Terron, M.C.Khandokar, Y.Aragao, D.Hardy, J.M.Radjainia, M.Jimenez-Zaragoza, M.de Pablo, P.J.Coulibaly, F.Luque, D.Raidal, S.R.Forwood, J.K.

(2016) Nat Commun 7: 13014-13014

  • DOI: 10.1038/ncomms13014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The assembly and regulation of viral capsid proteins into highly ordered macromolecular complexes is essential for viral replication. Here, we utilize crystal structures of the capsid protein from the smallest and simplest known viruses capable of au ...

    The assembly and regulation of viral capsid proteins into highly ordered macromolecular complexes is essential for viral replication. Here, we utilize crystal structures of the capsid protein from the smallest and simplest known viruses capable of autonomously replicating in animal cells, circoviruses, to establish structural and mechanistic insights into capsid morphogenesis and regulation. The beak and feather disease virus, like many circoviruses, encode only two genes: a capsid protein and a replication initiation protein. The capsid protein forms distinct macromolecular assemblies during replication and here we elucidate these structures at high resolution, showing that these complexes reverse the exposure of the N-terminal arginine rich domain responsible for DNA binding and nuclear localization. We show that assembly of these complexes is regulated by single-stranded DNA (ssDNA), and provide a structural basis of capsid assembly around single-stranded DNA, highlighting novel binding interfaces distinct from the highly positively charged N-terminal ARM domain.


    Organizational Affiliation

    Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.,Centro Nacional de Microbiología/ISCIII, Majadahonda, Madrid 28220, Spain.,School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2678, Australia.,School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.,Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia.,Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia.,Insituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beak and feather disease virus capsid protein
E, A, B, C, D
257Beak and feather disease virusMutation(s): 0 
Gene Names: Cap
Find proteins for A0A023R6W2 (Beak and feather disease virus)
Go to UniProtKB:  A0A023R6W2
Entity ID: 2
MoleculeChainsLengthOrganism
single stranded DNAF,G,H,I,J30synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 377.280α = 90.00
b = 377.280β = 90.00
c = 377.280γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references