5A9A

Crystal structure of Simulium ubiquitum CPV20 polyhedra


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Polyhedra Structures and the Evolution of the Insect Viruses.

Ji, X.Axford, D.Owen, R.Evans, G.Ginn, H.M.Sutton, G.Stuart, D.I.

(2015) J.Struct.Biol. 192: 88

  • DOI: 10.1016/j.jsb.2015.08.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polyhedra represent an ancient system used by a number of insect viruses to protect virions during long periods of environmental exposure. We present high resolution crystal structures of polyhedra for seven previously uncharacterised types of cypovi ...

    Polyhedra represent an ancient system used by a number of insect viruses to protect virions during long periods of environmental exposure. We present high resolution crystal structures of polyhedra for seven previously uncharacterised types of cypoviruses, four using ab initio selenomethionine phasing (two of these required over 100 selenomethionine crystals each). Approximately 80% of residues are structurally equivalent between all polyhedrins (pairwise rmsd ⩽ 1.5 Å), whilst pairwise sequence identities, based on structural alignment, are as little as 12%. These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability. The conservation of crystal contacts is maintained across most of the molecular surface, except for a dispensable virus recognition domain. By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes. Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.


    Organizational Affiliation

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POLYHEDRIN
A
243Simulium ubiquitum cypovirusMutation(s): 0 
Find proteins for Q0MX25 (Simulium ubiquitum cypovirus)
Go to UniProtKB:  Q0MX25
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UTP
Query on UTP

Download SDF File 
Download CCD File 
A
URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 103.360α = 90.00
b = 103.360β = 90.00
c = 103.360γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
PHASERphasing
xia2data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references