2QQP

Crystal Structure of Authentic Providence Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Work: 0.285 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    2QQP

  • 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 that determine their quasi equivalent capsid structures ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Large Capsid proteinA, C, E, G556Providence virusMutation(s): 0 
UniProt
Find proteins for Q80IX5 (Providence virus (isolate Helicoverpa zea/United States/vFLM1/-))
Explore Q80IX5 
Go to UniProtKB:  Q80IX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80IX5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small capsid proteinB, D, F, H75Providence virusMutation(s): 0 
UniProt
Find proteins for Q80IX5 (Providence virus (isolate Helicoverpa zea/United States/vFLM1/-))
Explore Q80IX5 
Go to UniProtKB:  Q80IX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80IX5
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(*UP*UP*UP*U)-3')I [auth R]4N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth A],
K [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Work: 0.285 
  • R-Value Observed: 0.285 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 659.79α = 90
b = 434.07β = 126.13
c = 415.85γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
GLRFphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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