1NOV

NODAMURA VIRUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Work: 0.296 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Resolution of space-group ambiguity and structure determination of nodamura virus to 3.3 A resolution from pseudo-R32 (monoclinic) crystals.

Zlotnick, A.Natarajan, P.Munshi, S.Johnson, J.E.

(1997) Acta Crystallogr.,Sect.D 53: 738-746

  • DOI: 10.1107/S0907444997007427

  • PubMed Abstract: 
  • Monoclinic crystals of nodamura virus (NOV) have two virus molecules per asymmetric unit. Packing analysis reveals a pseudo-rhombohedral (pseudo-C2 monoclinic) arrangement of particles in the actual P2(1) space group (a = 562.1, b = 354.1, c = 612.8 ...

    Monoclinic crystals of nodamura virus (NOV) have two virus molecules per asymmetric unit. Packing analysis reveals a pseudo-rhombohedral (pseudo-C2 monoclinic) arrangement of particles in the actual P2(1) space group (a = 562.1, b = 354.1, c = 612.8 A, beta = 110.9 degrees ). The R32 symmetry is broken rotationally and translationally. The pseudo-symmetry of the unit cell results in three possible monoclinic origins and also restrains the four particles in the unit cell to similar orientations. NOV particles deviate by less than 3 degrees from the ideal orientations, causing overlap of peaks in the rotation function and the generation of peaks that were not interpretable as particle symmetry elements. The space-group ambiguity was resolved by analysing the relationship between the particle orientations determined by high-resolution rotation functions and the attenuation of peak heights in native Patterson maps. Particles were centered less than 1 A from the R32 special positions. Three different approaches were required to identify the correct particle center. Following the solutions of the rotation and translation problems, phases were computed using the coordinates of flock house virus (FHV), another member of this virus family. The phases were improved by real-space molecular averaging with a 120-fold non-crystallographic symmetry and by solvent flattening with a spherical mask. The final model for the NOV structure was built using the 3.3 A averaged map. While the overall subunit structure was very similar to that of other nodaviruses, FHV and black beetle virus, NOV showed distinct structural features near particle threefold and quasi-threefold axes and at the protein-RNA interfaces that are consistent with phenotype differences among the related viruses.


    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
    • Ordered Duplex RNA Controls Capsid Architecture in an Icosahedral Animal Virus
      Fisher, A.J.,Johnson, J.E.
      (1993) Nature 361: 176
    • A Monoclinic Crystal with R32 Pseudo-Symmetry: A Preliminary Report of Nodamura Virus Structure Determination
      Zlotnick, A.,Mckinney, B.R.,Munshi, S.,Bibler, J.,Rossmann, M.G.,Johnson, J.E.
      (1993) Acta Crystallogr.,Sect.D 49: 580
    • 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


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NODAMURA VIRUS COAT PROTEINS
A, B, C
355Nodamura virus (strain Mag115)Gene Names: alpha
EC: 3.4.23.44
Find proteins for P12871 (Nodamura virus (strain Mag115))
Go to UniProtKB:  P12871
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NODAMURA VIRUS COAT PROTEINS
D, E, F
44Nodamura virus (strain Mag115)Gene Names: alpha
EC: 3.4.23.44
Find proteins for P12871 (Nodamura virus (strain Mag115))
Go to UniProtKB:  P12871
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Work: 0.296 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 562.090α = 90.00
b = 354.130β = 110.89
c = 612.770γ = 90.00
Software Package:
Software NamePurpose
PURDUEdata reduction
X-PLORmodel building
X-PLORrefinement
OSCdata reduction
OSCdata collection
OSCdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-30
    Type: Advisory