5A8S

Crystal structure of Antheraea mylitta CPV4 polyhedra type 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.123 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    5A8S, 5A8T, 5A8U, 5A8V, 5A96, 5A98, 5A99, 5A9A, 5A9B, 5A9C, 5A9P

  • 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 cypoviruses, four using ab initio selenomethionine phasing (two of these required over 100 selenomethionine crystals each) ...

    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; Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom. Electronic address: dave@strubi.ox.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLYHEDRINA254Antheraea mylitta cypovirus 4Mutation(s): 1 
UniProt
Find proteins for Q67G25 (Antheraea mylitta cypovirus 4)
Explore Q67G25 
Go to UniProtKB:  Q67G25
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.123 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.682α = 90
b = 101.682β = 90
c = 101.682γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other