1EV1

ECHOVIRUS 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6RJF


Literature

Structure determination of echovirus 1.

Filman, D.J., Wien, M.W., Cunningham, J.A., Bergelson, J.M., Hogle, J.M.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1261-1272

  • DOI: 10.1107/s0907444998002790
  • Primary Citation of Related Structures:  
    1EV1

  • PubMed Abstract: 

    • The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483 ...

    The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 A. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 A resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved.

    Related Citations: 
    • A Pseudo-Cell Based Approach to Efficient Crystallographic Refinement of Viruses
      Jacobson, D.H., Hogle, J.M., Filman, D.J.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 693
    Organizational Affiliation: 

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ECHOVIRUS 1A [auth 1]281Echovirus E1Mutation(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 O91734 (Echovirus 1 (strain Human/Egypt/Farouk/1951))
Explore O91734 
Go to UniProtKB:  O91734
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ECHOVIRUS 1B [auth 2]254Echovirus E1Mutation(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 O91734 (Echovirus 1 (strain Human/Egypt/Farouk/1951))
Explore O91734 
Go to UniProtKB:  O91734
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ECHOVIRUS 1C [auth 3]239Echovirus E1Mutation(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 O91734 (Echovirus 1 (strain Human/Egypt/Farouk/1951))
Explore O91734 
Go to UniProtKB:  O91734
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ECHOVIRUS 1D [auth 4]68Echovirus E1Mutation(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 O91734 (Echovirus 1 (strain Human/Egypt/Farouk/1951))
Explore O91734 
Go to UniProtKB:  O91734
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM
Download Ideal Coordinates CCD File 
 E [auth 1]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N		 Ligand Interaction
MYR
Query on MYR
Download Ideal Coordinates CCD File 
 F [auth 4]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 472.15α = 90
b = 483.2β = 90
c = 352.45γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance