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PDBsum entry 1eah

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protein ligands Protein-protein interface(s) links
Virus PDB id
1eah
Jmol
Contents
Protein chains
272 a.a. *
262 a.a. *
235 a.a. *
68 a.a. *
Ligands
MYR
SC4
Waters ×271
* Residue conservation analysis
PDB id:
1eah
Name: Virus
Title: Pv2l complexed with antiviral agent sch48973
Structure: Poliovirus type 2 coat proteins vp1 to vp4. Chain: 1. Engineered: yes. Poliovirus type 2 coat proteins vp1 to vp4. Chain: 2. Engineered: yes. Poliovirus type 2 coat proteins vp1 to vp4. Chain: 3. Engineered: yes.
Source: Human poliovirus 2. Organism_taxid: 12083. Strain: lansing. Cell_line: hela cells. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hela cells. Expression_system_cell_line: hela cells
Resolution:
2.90Å     R-factor:   0.185    
Authors: K.Lentz,E.Arnold
Key ref:
K.N.Lentz et al. (1997). Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of three poliovirus serotypes. Structure, 5, 961-978. PubMed id: 9261087 DOI: 10.1016/S0969-2126(97)00249-9
Date:
22-Jul-97     Release date:   16-Sep-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06210  (POLG_POL2L) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2207 a.a.
272 a.a.
Protein chain
No UniProt id for this chain
Struc: 262 a.a.
Protein chain
Pfam   ArchSchema ?
P06210  (POLG_POL2L) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2207 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P06210  (POLG_POL2L) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2207 a.a.
68 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains 1, 3, 4: E.C.2.7.7.48  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
   Enzyme class 3: Chains 1, 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 4: Chains 1, 3, 4: E.C.3.4.22.29  - Picornain 2A.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
   Enzyme class 5: Chains 1, 3, 4: E.C.3.6.1.15  - Nucleoside-triphosphate phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NTP + H2O = NDP + phosphate
NTP
+ H(2)O
= NDP
+ phosphate
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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral capsid   1 term 
  Biochemical function     structural molecule activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(97)00249-9 Structure 5:961-978 (1997)
PubMed id: 9261087  
 
 
Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of three poliovirus serotypes.
K.N.Lentz, A.D.Smith, S.C.Geisler, S.Cox, P.Buontempo, A.Skelton, J.DeMartino, E.Rozhon, J.Schwartz, V.Girijavallabhan, J.O'Connell, E.Arnold.
 
  ABSTRACT  
 
BACKGROUND: Polioviruses are human pathogens and the causative agents of poliomyelitis. Polioviruses are icosahedral single-stranded RNA viruses, which belong to the picornavirus family, and occur as three distinct serotypes. All three serotypes of poliovirus can infect primates, but only type 2 can infect mice. The crystal structures of a type 1 and a type 3 poliovirus are already known. Structural studies of poliovirus type 2 Lansing (PV2L) were initiated to try to enhance our understanding of the differences in host range specificity, antigenicity and receptor binding among the three serotypes of poliovirus. RESULTS: The crystal structure of the mouse neurovirulent PV2L complexed with a potent antiviral agent, SCH48973, was determined at 2.9 A resolution. Structural differences among the three poliovirus serotypes occur primarily in the loop regions of the viral coat proteins (VPs), most notably in the loops of VP1 that cluster near the fivefold axes of the capsid, where the BC loop of PV2L is disordered. Unlike other known structures of enteroviruses, the entire polypeptide chain of PV2L VP4 is visible in the electron density and RNA bases are observed stacking with conserved aromatic residues (Tyr4020 and Phe4046) of VP4. The broad-spectrum antiviral agent SCH48973 is observed binding in a pocket within the beta-barrel of VP1, in approximately the same location that natural 'pocket factors' bind to polioviruses. SCH48973 forms predominantly hydrophobic interactions with the pocket residues. CONCLUSIONS: Some of the conformational changes required for infectivity and involved in the control of capsid stability and neurovirulence in mice may occur in the vicinity of the fivefold axis of the poliovirus, where there are significant structural differences among the three poliovirus serotypes in the surface exposed loops of VP1 (BC, DE, and HI). A surface depression is located at the fivefold axis of PV2L that is not present in the other two poliovirus serotypes. The observed interaction of RNA with VP4 supports the observation that loss of VP4 ultimately leads to the loss of viral RNA. A model is proposed that suggests dual involvement of the virion fivefold and pseudo-threefold axes in receptor-mediated initiation of infection by picornaviruses.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The antiviral agent in the pocket of VP1 and its location relative to the canyon region [118]. VP1 and VP3 are shown in blue and red ribbon representation, respectively. SCH48973 is colored according to atom type: carbon atoms green; oxygen atoms red; and chlorine atoms cyan. Sidechains near the inhibitor are shown in yellow. All the protein contacts to SCH48973 are hydrophobic in nature.
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 961-978) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21325720 A.Janner (2011).
Form, symmetry and packing of biomacromolecules. III. Antigenic, receptor and contact binding sites in picornaviruses.
  Acta Crystallogr A, 67, 174-189.  
19515771 S.van der Sanden, M.A.Pallansch, J.van de Kassteele, N.El-Sayed, R.W.Sutter, M.Koopmans, and H.van der Avoort (2009).
Shedding of vaccine viruses with increased antigenic and genetic divergence after vaccination of newborns with monovalent type 1 oral poliovirus vaccine.
  J Virol, 83, 8693-8704.  
18579607 F.B.Riquet, C.Blanchard, S.Jegouic, J.Balanant, S.Guillot, M.A.Vibet, M.Rakoto-Andrianarivelo, and F.Delpeyroux (2008).
Impact of exogenous sequences on the characteristics of an epidemic type 2 recombinant vaccine-derived poliovirus.
  J Virol, 82, 8927-8932.  
18029287 M.M.Sandager, J.L.Nugent, W.L.Schulz, R.P.Messner, and P.E.Tam (2008).
Interactions between multiple genetic determinants in the 5' UTR and VP1 capsid control pathogenesis of chronic post-viral myopathy caused by coxsackievirus B1.
  Virology, 372, 35-47.  
19011098 P.Zhang, S.Mueller, M.C.Morais, C.M.Bator, V.D.Bowman, S.Hafenstein, E.Wimmer, and M.G.Rossmann (2008).
Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses.
  Proc Natl Acad Sci U S A, 105, 18284-18289.
PDB codes: 3eow 3epc 3epd 3epf 3uro
18480448 S.Khan, X.Peng, J.Yin, P.Zhang, and E.Wimmer (2008).
Characterization of the New World monkey homologues of human poliovirus receptor CD155.
  J Virol, 82, 7167-7179.  
18085822 M.Rakoto-Andrianarivelo, S.Guillot, J.Iber, J.Balanant, B.Blondel, F.Riquet, J.Martin, O.Kew, B.Randriamanalina, L.Razafinimpiasa, D.Rousset, and F.Delpeyroux (2007).
Co-circulation and evolution of polioviruses and species C enteroviruses in a district of Madagascar.
  PLoS Pathog, 3, e191.  
17537857 M.S.Kim, and V.R.Racaniello (2007).
Enterovirus 70 receptor utilization is controlled by capsid residues that also regulate host range and cytopathogenicity.
  J Virol, 81, 8648-8655.  
16537593 C.C.Burns, J.Shaw, R.Campagnoli, J.Jorba, A.Vincent, J.Quay, and O.Kew (2006).
Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region.
  J Virol, 80, 3259-3272.  
16868986 Y.Y.Ke, Y.C.Chen, and T.H.Lin (2006).
Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies.
  J Comput Chem, 27, 1556-1570.  
16153180 O.M.Kew, R.W.Sutter, E.M.de Gourville, W.R.Dowdle, and M.A.Pallansch (2005).
Vaccine-derived polioviruses and the endgame strategy for global polio eradication.
  Annu Rev Microbiol, 59, 587-635.  
14990711 E.A.Hewat, and D.Blaas (2004).
Cryoelectron microscopy analysis of the structural changes associated with human rhinovirus type 14 uncoating.
  J Virol, 78, 2935-2942.  
15006797 M.Chambon, C.Archimbaud, J.L.Bailly, J.M.Gourgand, F.Charbonné, and H.Peigue-Lafeuille (2004).
Virucidal efficacy of glutaraldehyde against enteroviruses is related to the location of lysine residues in exposed structures of the VP1 capsid protein.
  Appl Environ Microbiol, 70, 1717-1722.  
15452226 Y.Zhang, A.A.Simpson, R.M.Ledford, C.M.Bator, S.Chakravarty, G.A.Skochko, T.M.Demenczuk, A.Watanyar, D.C.Pevear, and M.G.Rossmann (2004).
Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds.
  J Virol, 78, 11061-11069.
PDB codes: 1na1 1ncq 1ncr 1nd2 1nd3
12663789 Y.He, S.Mueller, P.R.Chipman, C.M.Bator, X.Peng, V.D.Bowman, S.Mukhopadhyay, E.Wimmer, R.J.Kuhn, and M.G.Rossmann (2003).
Complexes of poliovirus serotypes with their common cellular receptor, CD155.
  J Virol, 77, 4827-4835.
PDB code: 1nn8
12121655 J.Ding, A.D.Smith, S.C.Geisler, X.Ma, G.F.Arnold, and E.Arnold (2002).
Crystal structure of a human rhinovirus that displays part of the HIV-1 V3 loop and induces neutralizing antibodies against HIV-1.
  Structure, 10, 999.
PDB code: 1k5m
12142481 J.M.Hogle (2002).
Poliovirus cell entry: common structural themes in viral cell entry pathways.
  Annu Rev Microbiol, 56, 677-702.  
11134308 A.Airaksinen, M.Roivainen, and T.Hovi (2001).
Coxsackievirus A9 VP1 mutants with enhanced or hindered A particle formation and decreased infectivity.
  J Virol, 75, 952-960.  
11160747 C.Xiao, C.M.Bator, V.D.Bowman, E.Rieder, Y.He, B.Hébert, J.Bella, T.S.Baker, E.Wimmer, R.J.Kuhn, and M.G.Rossmann (2001).
Interaction of coxsackievirus A21 with its cellular receptor, ICAM-1.
  J Virol, 75, 2444-2451.  
11689657 Q.Jia, J.M.Hogle, T.Hashikawa, and A.Nomoto (2001).
Molecular genetic analysis of revertants from a poliovirus mutant that is specifically adapted to the mouse spinal cord.
  J Virol, 75, 11766-11772.  
11182317 S.K.Tsang, J.Cheh, L.Isaacs, D.Joseph-McCarthy, S.K.Choi, D.C.Pevear, G.M.Whitesides, and J.M.Hogle (2001).
A structurally biased combinatorial approach for discovering new anti-picornaviral compounds.
  Chem Biol, 8, 33-45.  
10627545 D.M.Belnap, D.J.Filman, B.L.Trus, N.Cheng, F.P.Booy, J.F.Conway, S.Curry, C.N.Hiremath, S.K.Tsang, A.C.Steven, and J.M.Hogle (2000).
Molecular tectonic model of virus structural transitions: the putative cell entry states of poliovirus.
  J Virol, 74, 1342-1354.  
10047583 L.Liljas (1999).
Virus assembly.
  Curr Opin Struct Biol, 9, 129-134.  
10089503 D.J.Filman, M.W.Wien, J.A.Cunningham, J.M.Bergelson, and J.M.Hogle (1998).
Structure determination of echovirus 1.
  Acta Crystallogr D Biol Crystallogr, 54, 1261-1272.
PDB code: 1ev1
9631286 J.J.Rux, and R.M.Burnett (1998).
Spherical viruses.
  Curr Opin Struct Biol, 8, 142-149.  
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.