2QQP

Crystal Structure of Authentic Providence Virus

• PDB DOI:  https://doi.org/10.2210/pdb2QQP/pdb
• NAKB: 2QQP

• Classification: VIRUS
• Organism(s): Providence virus
• Mutation(s): No 


• Deposited: 2007-07-26 Released: 2009-01-20 
• Deposition Author(s): Speir, J.A., Taylor, D.J., Johnson, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Work: 0.285 
• R-Value Observed: 0.285 

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

• PubMed: 20541507 
• DOI: https://doi.org/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 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 480-mer - A240B180C60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 273.84 kDa 
• Atom Count: 16,634 
• Modelled Residue Count: 2,191 
• Deposited Residue Count: 2,528 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large Capsid protein	A, C, E, G	556	Providence virus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small capsid protein	B, D, F, H	75	Providence virus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*UP*U)-3')	I [auth R]	4	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	J [auth A], K [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 659.79	α = 90
b = 434.07	β = 126.13
c = 415.85	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
GLRF	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Speir, J.A., Taylor, D.J., Johnson, J.E.

Revision History  

• 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