4S1K

Structure of Uranotaenia sapphirina cypovirus (CPV17) polyhedrin at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data.

Ginn, H.M.Messerschmidt, M.Ji, X.Zhang, H.Axford, D.Gildea, R.J.Winter, G.Brewster, A.S.Hattne, J.Wagner, A.Grimes, J.M.Evans, G.Sauter, N.K.Sutton, G.Stuart, D.I.

(2015) Nat Commun 6: 6435-6435

  • DOI: 10.1038/ncomms7435
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cy ...

    The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and protein core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyhedrin
A
237Uranotaenia sapphirina cypovirusMutation(s): 0 
Find proteins for Q5EK29 (Uranotaenia sapphirina cypovirus)
Go to UniProtKB:  Q5EK29
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.148 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 104.879α = 90.00
b = 104.879β = 90.00
c = 104.879γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DIALSdata scaling
REFMACrefinement
DIALSdata reduction
DIALSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release