1MEC

CONFORMATIONAL VARIABILITY OF A PICORNAVIRUS CAPSID: PH-DEPENDENT STRUCTURAL CHANGES OF MENGO VIRUS RELATED TO ITS HOST RECEPTOR ATTACHMENT SITE AND DISASSEMBLY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conformational variability of a picornavirus capsid: pH-dependent structural changes of Mengo virus related to its host receptor attachment site and disassembly.

Kim, S.Boege, U.Krishnaswamy, S.Minor, I.Smith, T.J.Luo, M.Scraba, D.G.Rossmann, M.G.

(1990) Virology 175: 176-190


  • PubMed Abstract: 
  • The structure of Mengo virus had been determined from crystals grown in the presence of 100 mM phosphate buffer at pH 7.4. It is shown that Mengo virus is poorly infectious at the phosphate concentration similar to that in which it was crystallized. ...

    The structure of Mengo virus had been determined from crystals grown in the presence of 100 mM phosphate buffer at pH 7.4. It is shown that Mengo virus is poorly infectious at the phosphate concentration similar to that in which it was crystallized. Maximal infectivity is achieved at 10 mM phosphate or less in physiological saline. The phosphate effect is ameliorated when the pH is lowered to 4.6. Although it has not been possible to study the crystal structure of the virus at low phosphate concentrations, it is shown that increasing the Cl- concentration at pH 6.2 or decreasing the pH to 4.6 causes substantial conformational changes confined to the "pit," a deep surface depression. These structural changes involve a movement of the "FMDV loop" (GH loop) in VP1, an ordering of the "VP3 loop" (GH loop in VP3) between 3176 and 3182, the displacement of a bound phosphate near the "FMDV loop" (GH loop in VP1), and movement of the carboxy terminus of VP2. The changes in conformation are correlated with the dissociation of the virion into pentamers at pH 6.2 and 150 mM Cl-. The localization of the conformational changes and the correlated role of the phosphate in controlling infectivity support the hypothesis that the "pit" is the receptor attachment site.


    Related Citations: 
    • Implications of the Picornavirus Capsid Structure for Polyprotein Processing
      Arnold, E.,Luo, M.,Vriend, G.,Rossmann, M.G.,Palmenberg, A.C.,Parks, G.D.,Nicklin, M.J.H.,Wimmer, E.
      (1987) Proc.Natl.Acad.Sci.USA 84: 21
    • Picornaviruses of Two Different Genera Have Similar Structures
      Luo, M.,Arnold, E.,Erickson, J.W.,Rossmann, M.G.,Boege, U.,Scraba, D.G.
      (1984) J.Mol.Biol. 180: 703
    • Structural Refinement and Analysis of Mengo Virus
      Krishnaswamy, S.,Rossmann, M.G.
      (1990) J.Mol.Biol. 211: 803
    • The Atomic Structure of Mengo Virus at 3.0 Angstroms Resolution
      Luo, M.,Vriend, G.,Kamer, G.,Minor, I.,Arnold, E.,Rossmann, M.G.,Boege, U.,Scraba, D.G.,Duke, G.M.,Palmenberg, A.C.
      (1987) Science 235: 182
    • Structure Determination of Mengo Virus
      Luo, M.,Vriend, G.,Kamer, G.,Rossmann, M.G.
      (1989) Acta Crystallogr.,Sect.B 45: 85
    • The Structure of a Human Common Cold Virus (Rhinovirus 14) and its Evolutionary Relations to Other Viruses
      Rossmann, M.G.,Arnold, E.,Erickson, J.W.,Frankenberger, E.A.,Griffith, J.P.,Hecht, H.-J.,Johnson, J.E.,Kamer, G.,Luo, M.,Vriend, G.,Mosser, A.G.,Palmenberg, A.C.,Rueckert, R.R.,Sherry, B.
      (1986) Chem.Scr. 26: 313
    • Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
      Rossmann, M.G.,Arnold, E.,Erickson, J.W.,Frankenberger, E.A.,Griffith, J.P.,Hecht, H.-J.,Johnson, J.E.,Kamer, G.,Luo, M.,Mosser, A.G.,Rueckert, R.R.,Sherry, B.,Vriend, G.
      (1985) Nature 317: 145


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)
1
274Mengo encephalomyocarditis virusMutation(s): 0 
Find proteins for P12296 (Mengo encephalomyocarditis virus)
Go to UniProtKB:  P12296
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MENGO VIRUS COAT PROTEIN (SUBUNIT VP2)
2
256Mengo encephalomyocarditis virusMutation(s): 0 
Find proteins for P12296 (Mengo encephalomyocarditis virus)
Go to UniProtKB:  P12296
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)
3
231Mengo encephalomyocarditis virusMutation(s): 0 
Find proteins for P12296 (Mengo encephalomyocarditis virus)
Go to UniProtKB:  P12296
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)
4
70Mengo encephalomyocarditis virusMutation(s): 0 
Find proteins for P12296 (Mengo encephalomyocarditis virus)
Go to UniProtKB:  P12296
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
2
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 439.800α = 90.00
b = 426.900β = 90.00
c = 421.200γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1992-01-17 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Rossmann, M.G.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other