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PDBsum entry 1mec
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protein ligands Protein-protein interface(s) links
Virus PDB id
1mec

 

 

 

 

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Contents
Protein chains
274 a.a. *
256 a.a. *
231 a.a. *
62 a.a. *
Ligands
PO4 ×2
Waters ×296
* Residue conservation analysis
PDB id:
1mec
Name: Virus
Title: Conformational variability of a picornavirus capsid: ph-dependent structural changes of mengo virus related to its host receptor attachment site and disassembly
Structure: Mengo virus coat protein (subunit vp1). Chain: 1. Engineered: yes. Mengo virus coat protein (subunit vp2). Chain: 2. Engineered: yes. Mengo virus coat protein (subunit vp1). Chain: 3. Engineered: yes.
Source: Mengo virus. Organism_taxid: 12107. Organism_taxid: 12107
Resolution:
3.20Å     R-factor:   not given    
Authors: M.G.Rossmann
Key ref: S.Kim et al. (1990). Conformational variability of a picornavirus capsid: pH-dependent structural changes of Mengo virus related to its host receptor attachment site and disassembly. Virology, 175, 176-190. PubMed id: 2155508
Date:
17-Jan-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P12296  (POLG_ENMGO) -  Genome polyprotein from Mengo encephalomyocarditis virus
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2293 a.a.
274 a.a.*
Protein chain
Pfam   ArchSchema ?
P12296  (POLG_ENMGO) -  Genome polyprotein from Mengo encephalomyocarditis virus
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2293 a.a.
256 a.a.
Protein chain
Pfam   ArchSchema ?
P12296  (POLG_ENMGO) -  Genome polyprotein from Mengo encephalomyocarditis virus
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2293 a.a.
231 a.a.*
Protein chain
Pfam   ArchSchema ?
P12296  (POLG_ENMGO) -  Genome polyprotein from Mengo encephalomyocarditis virus
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2293 a.a.
62 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chains 1, 2, 3, 4: E.C.2.7.7.48  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
RNA(n)
 + ribonucleoside 5'-triphosphate
 = RNA(n+1)
Bound ligand (Het Group name = PO4)
matches with 55.56% similarity 		+ diphosphate
   Enzyme class 2: Chains 1, 2, 3, 4: E.C.3.4.22.28  - picornain 3C.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
   Enzyme class 3: Chains 1, 2, 3, 4: E.C.3.6.4.13  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
 + H2O
 = ADP
 + phosphate
 + H(+)
Bound ligand (Het Group name = PO4)
corresponds exactly
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Virology 175:176-190 (1990)
PubMed id: 2155508  
 
 
Conformational variability of a picornavirus capsid: pH-dependent structural changes of Mengo virus related to its host receptor attachment site and disassembly.
S.Kim, U.Boege, S.Krishnaswamy, I.Minor, T.J.Smith, M.Luo, D.G.Scraba, M.G.Rossmann.
 
  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. 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22388738 X.Wang, W.Peng, J.Ren, Z.Hu, J.Xu, Z.Lou, X.Li, W.Yin, X.Shen, C.Porta, T.S.Walter, G.Evans, D.Axford, R.Owen, D.J.Rowlands, J.Wang, D.I.Stuart, E.E.Fry, and Z.Rao (2012).
A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.
  Nat Struct Mol Biol, 19, 424-429.
PDB codes: 3vbf 3vbh 3vbo 3vbr 3vbs 3vbu
19816570 T.J.Tuthill, K.Harlos, T.S.Walter, N.J.Knowles, E.Groppelli, D.J.Rowlands, D.I.Stuart, and E.E.Fry (2009).
Equine rhinitis A virus and its low pH empty particle: clues towards an aphthovirus entry mechanism?
  PLoS Pathog, 5, e1000620.
PDB codes: 2wff 2ws9
16575521 H.L.Lipton, A.S.Kumar, S.Hertzler, and H.V.Reddi (2006).
Differential usage of carbohydrate co-receptors influences cellular tropism of Theiler's murine encephalomyelitis virus infection of the central nervous system.
  Glycoconj J, 23, 39-49.  
15280494 A.S.Kumar, H.V.Reddi, A.Y.Kung, M.Dal Canto, and H.L.Lipton (2004).
Virus persistence in an animal model of multiple sclerosis requires virion attachment to sialic acid coreceptors.
  J Virol, 78, 8860-8867.  
15331714 G.Sánchez, L.Aragonès, M.I.Costafreda, E.Ribes, A.Bosch, and R.M.Pintó (2004).
Capsid region involved in hepatitis A virus binding to glycophorin A of the erythrocyte membrane.
  J Virol, 78, 9807-9813.  
12110211 M.G.Rossmann, Y.He, and R.J.Kuhn (2002).
Picornavirus-receptor interactions.
  Trends Microbiol, 10, 324-331.  
11101504 E.A.Hewat, E.Neumann, J.F.Conway, R.Moser, B.Ronacher, T.C.Marlovits, and D.Blaas (2000).
The cellular receptor to human rhinovirus 2 binds around the 5-fold axis and not in the canyon: a structural view.
  EMBO J, 19, 6317-6325.  
10644372 S.Hertzler, M.Luo, and H.L.Lipton (2000).
Mutation of predicted virion pit residues alters binding of Theiler's murine encephalomyelitis virus to BHK-21 cells.
  J Virol, 74, 1994-2004.  
  9371580 J.S.Parker, and C.R.Parrish (1997).
Canine parvovirus host range is determined by the specific conformation of an additional region of the capsid.
  J Virol, 71, 9214-9222.  
  8794359 S.Curry, M.Chow, and J.M.Hogle (1996).
The poliovirus 135S particle is infectious.
  J Virol, 70, 7125-7131.  
  7498760 M.C.Ekechukwu, D.J.Oberste, and B.A.Fane (1995).
Host and phi X 174 mutations affecting the morphogenesis or stabilization of the 50S complex, a single-stranded DNA synthesizing intermediate.
  Genetics, 140, 1167-1174.  
7773791 M.Smyth, J.Tate, E.Hoey, C.Lyons, S.Martin, and D.Stuart (1995).
Implications for viral uncoating from the structure of bovine enterovirus.
  Nat Struct Biol, 2, 224-231.
PDB code: 1bev
  7983739 S.Curry, C.C.Abrams, E.Fry, J.C.Crowther, G.J.Belsham, D.I.Stuart, and A.M.King (1995).
Viral RNA modulates the acid sensitivity of foot-and-mouth disease virus capsids.
  J Virol, 69, 430-438.  
8093643 N.H.Olson, P.R.Kolatkar, M.A.Oliveira, R.H.Cheng, J.M.Greve, A.McClelland, T.S.Baker, and M.G.Rossmann (1993).
Structure of a human rhinovirus complexed with its receptor molecule.
  Proc Natl Acad Sci U S A, 90, 507-511.  
1312722 M.Luo, C.He, K.S.Toth, C.X.Zhang, and H.L.Lipton (1992).
Three-dimensional structure of Theiler murine encephalomyelitis virus (BeAn strain).
  Proc Natl Acad Sci U S A, 89, 2409-2413.
PDB code: 1tmf
  1331498 S.F.Chang, J.Y.Sgro, and C.R.Parrish (1992).
Multiple amino acids in the capsid structure of canine parvovirus coordinately determine the canine host range and specific antigenic and hemagglutination properties.
  J Virol, 66, 6858-6867.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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