1HXS

CRYSTAL STRUCTURE OF MAHONEY STRAIN OF POLIOVIRUS AT 2.2A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution.

Miller, S.T.Hogle, J.M.Filman, D.J.

(2001) J Mol Biol 307: 499-512

  • DOI: 10.1006/jmbi.2001.4485
  • Primary Citation of Related Structures:  
    1HXS

  • PubMed Abstract: 
  • A genetic algorithm-based computational method for the ab initio phasing of diffraction data from crystals of symmetric macromolecular structures, such as icosahedral viruses, has been implemented and applied to authentic data from the P1/Mahoney str ...

    A genetic algorithm-based computational method for the ab initio phasing of diffraction data from crystals of symmetric macromolecular structures, such as icosahedral viruses, has been implemented and applied to authentic data from the P1/Mahoney strain of poliovirus. Using only single-wavelength native diffraction data, the method is shown to be able to generate correct phases, and thus electron density, to 3.0 A resolution. Beginning with no advance knowledge of the shape of the virus and only approximate knowledge of its size, the method uses a genetic algorithm to determine coarse, low-resolution (here, 20.5 A) models of the virus that obey the known non-crystallographic symmetry (NCS) constraints. The best scoring of these models are subjected to refinement and NCS-averaging, with subsequent phase extension to high resolution (3.0 A). Initial difficulties in phase extension were overcome by measuring and including all low-resolution terms in the transform. With the low-resolution data included, the method was successful in generating essentially correct phases and electron density to 6.0 A in every one of ten trials from different models identified by the genetic algorithm. Retrospective analysis revealed that these correct high-resolution solutions converged from a range of significantly different low-resolution phase sets (average differences of 59.7 degrees below 24 A). This method represents an efficient way to determine phases for icosahedral viruses, and has the advantage of producing phases free from model bias. It is expected that the method can be extended to other protein systems with high NCS.


    Related Citations: 
    • Ab initio Phasing of High-Symmetry Macromolecular Complexes: Successful Phasing of Authentic Poliovirus Data to 3.0A Resolution
      Miller, S.T., Hogle, J.M., Filman, D.J.
      () To be published --: --
    • A Genetic Algorithm for the ab initio phasing of Icosahedral Viruses
      Miller, S.T., Hogle, J.M., Filman, D.J.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 234
    • Structural Studies of Poliovirus Mutants that overcome receptor defects
      Wien, M.W., Curry, S., Filman, D.J., Hogle, J.M.
      (1997) Nat Struct Biol 4: 666
    • Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus
      Filman, D.J., Syed, R., Chow, M., Macadam, A.J., Minor, P.D., Hogle, J.M.
      (1989) EMBO J 8: 1567
    • Three-dimensional structure of poliovirus at 2.9A resolution
      Hogle, J.M., Chow, M., Filman, D.J.
      (1985) Science 229: 1358
    • Collection of very low resolution protein data
      Miller, S.T., Genova, J.G., Hogle, J.M.
      (1999) J Appl Crystallogr 32: 1183

    Organizational Affiliation

    Committee for Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GENOME POLYPROTEIN, COAT PROTEIN VP11302Human poliovirus 1 MahoneyMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GENOME POLYPROTEIN, COAT PROTEIN VP22272Human poliovirus 1 MahoneyMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GENOME POLYPROTEIN, COAT PROTEIN VP33237Human poliovirus 1 MahoneyMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
GENOME POLYPROTEIN, COAT PROTEIN VP4468Human poliovirus 1 MahoneyMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download CCD File 
1
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
MYR
Query on MYR

Download CCD File 
4
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 320.5α = 90
b = 355.25β = 90
c = 377.25γ = 90
Software Package:
Software NamePurpose
DJFmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
DJFphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description