2QQP

Crystal Structure of Authentic Providence Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evolution in action: N and C termini of subunits in related T = 4 viruses exchange roles as molecular switches.

Speir, J.A.Taylor, D.J.Natarajan, P.Pringle, F.M.Ball, L.A.Johnson, J.E.

(2010) Structure 18: 700-709

  • DOI: 10.1016/j.str.2010.03.010

  • PubMed Abstract: 
  • The T = 4 tetravirus and T = 3 nodavirus capsid proteins undergo closely similar autoproteolysis to produce the N-terminal beta and C-terminal, lipophilic gamma polypeptides. The gamma peptides and the N termini of beta also act as molecular switches ...

    The T = 4 tetravirus and T = 3 nodavirus capsid proteins undergo closely similar autoproteolysis to produce the N-terminal beta and C-terminal, lipophilic gamma polypeptides. The gamma peptides and the N termini of beta also act as molecular switches that determine their quasi equivalent capsid structures. The crystal structure of Providence virus (PrV), only the second of a tetravirus (the first was NomegaV), reveals conserved folds and cleavage sites, but the protein termini have completely different structures and the opposite functions of those in NomegaV. N termini of beta form the molecular switch in PrV, whereas gamma peptides play this role in NomegaV. PrV gamma peptides instead interact with packaged RNA at the particle two-folds by using a repeating sequence pattern found in only four other RNA- or membrane-binding proteins. The disposition of peptide termini in PrV is closely related to those in nodaviruses, suggesting that PrV may be closer to the primordial T = 4 particle than NomegaV.


    Related Citations: 
    • Providence virus: a new member of the Tetraviridae that infects cultured insect cells
      Pringle, F.M.,Johnson, K.N.,Goodman, C.L.,McIntosh, A.H.,Ball, L.A.
      (2003) Virology 306: 359


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Large Capsid protein
A, C, E, G
556Providence virusMutation(s): 0 
Find proteins for Q80IX5 (Providence virus)
Go to UniProtKB:  Q80IX5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small capsid protein
B, D, F, H
75Providence virusMutation(s): 0 
Find proteins for Q80IX5 (Providence virus)
Go to UniProtKB:  Q80IX5
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*UP*U)-3')R4N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Work: 0.285 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 659.790α = 90.00
b = 434.070β = 126.13
c = 415.850γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
CNSrefinement
Blu-Icedata collection
PDB_EXTRACTdata extraction
GLRFphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description