2BBV

THE REFINED THREE-DIMENSIONAL STRUCTURE OF AN INSECT VIRUS AT 2.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The refined three-dimensional structure of an insect virus at 2.8 A resolution.

Wery, J.P.Reddy, V.S.Hosur, M.V.Johnson, J.E.

(1994) J.Mol.Biol. 235: 565-586

  • DOI: 10.1006/jmbi.1994.1014

  • PubMed Abstract: 
  • The structure of the black beetle nodavirus has been refined at 2.8 A resolution by alternate use of restrained least-squares atomic coordinate refinement and phase refinement by real space averaging with the 5-fold non-crystallographic symmetry in t ...

    The structure of the black beetle nodavirus has been refined at 2.8 A resolution by alternate use of restrained least-squares atomic coordinate refinement and phase refinement by real space averaging with the 5-fold non-crystallographic symmetry in the crystal. The coordinates were also refined by simulated annealing. The final R-factor for all data with I/sigma(I) > 4 was 22.1%. A total of 7692 atoms were refined in one icosahedral asymmetric unit which included 273 oxygen atoms of ordered water molecules. Three identical gene products of 407 amino acids form one icosahedral asymmetric unit. Each is located in a structurally unique position, identified as A, B or C, consistent with a T = 3 quasi equivalent lattice. Icosahedral pentamers are formed by A subunits while B and C subunits alternate about icosahedral 3-fold axes to form quasi hexamers. Five calcium ions are located within the icosahedral asymmetric unit and stabilize the quasi 3-fold related intersubunit contacts between A, B and C. The final model consists of coordinates for residues 56 to 379 of all three subunits and residues 20 to 31 from the C subunit only. Atom positions for the sugar-phosphate backbone were modeled for ten nucleotides close to the icosahedral 2-fold axes. Symmetry equivalent polyribonucleotides form a helical duplex at each icosahedral 2-fold axis. The three subunits display an eight-stranded beta-barrel fold, very similar to the subunit structures observed in most other icosahedral RNA viruses analyzed. Quasi equivalence is regulated by the ordered RNA and residues 20 to 31 in the C subunit to form a "flat inter subunit contact" at icosahedral 2-fold joints. The RNA and polypeptide are disordered at the quasi 2-fold joints and this results in a "bent inter subunit contact". Although similar quaternary structures were seen in T = 3 plant viruses studied, RNA did not play a role as a molecular switch in those structures. The autocatalytic, post assembly, cleavage of the initial gene product at residue Asn363/Ala364 to form a stable and infectious particle is probably the result of an acid catalyzed main-chain hydrolysis in which Asp75 is the proton donor. The reaction is initiated by assembly which places Asp75 in a hydrophobic environment created by quaternary interactions which raises its pK to 5.6. The region in which the reaction occurs is formed by an internal helical bundle that has not been seen in other virus structures.


    Related Citations: 
    • Structural Homology Among Four Nodaviruses as Deduced by Sequencing and X-Ray Crystallography
      Kaesberg, P.,Dasgupta, R.,Sgro, J.-Y.,Wery, J.-P.,Selling, B.H.,Hosur, M.V.,Johnson, J.E.
      (1990) J.Mol.Biol. 214: 423
    • Structure of an Insect Virus at 3.0 Angstroms Resolution
      Hosur, M.V.,Schmidt, T.,Tucker, R.C.,Johnson, J.E.,Gallagher, T.M.,Selling, B.H.,Rueckert, R.R.
      (1987) Proteins 2: 167
    • Ordered Duplex RNA Controls Capsid Architecture in an Icosahedral Animal Virus
      Fisher, A.J.,Johnson, J.E.
      (1993) Nature 361: 176


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
A, B, C
363Black beetle virusMutation(s): 0 
Gene Names: alpha
Find proteins for P04329 (Black beetle virus)
Go to UniProtKB:  P04329
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
D, E, F
44Black beetle virusMutation(s): 0 
Gene Names: alpha
Find proteins for P04329 (Black beetle virus)
Go to UniProtKB:  P04329
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')N10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.221 
  • Space Group: P 42 3 2
Unit Cell:
Length (Å)Angle (°)
a = 362.000α = 90.00
b = 362.000β = 90.00
c = 362.000γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations