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PDBsum entry 1ar9

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protein ligands Protein-protein interface(s) links
Virus PDB id
1ar9
Jmol
Contents
Protein chains
283 a.a. *
268 a.a. *
235 a.a. *
60 a.a. *
Ligands
GLY-SER-SER-SER-
THR
MYR
SPH
Waters ×535
* Residue conservation analysis
PDB id:
1ar9
Name: Virus
Title: P1/mahoney poliovirus, single site mutant h2142y
Structure: P1/mahoney poliovirus. Chain: 0. Fragment: virus protomer. Engineered: yes. Mutation: yes. P1/mahoney poliovirus. Chain: 1. Fragment: virus protomer. Engineered: yes.
Source: Human poliovirus 1. Organism_taxid: 12081. Strain: mahoney. Strain: mahoney
Resolution:
2.90Å     R-factor:   0.244    
Authors: M.W.Wien,S.Curry,D.J.Filman,J.M.Hogle
Key ref: M.W.Wien et al. (1997). Structural studies of poliovirus mutants that overcome receptor defects. Nat Struct Biol, 4, 666-674. PubMed id: 9253417
Date:
11-Aug-97     Release date:   03-Dec-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2209 a.a.
283 a.a.
Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2209 a.a.
268 a.a.*
Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2209 a.a.
235 a.a.*
Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2209 a.a.
60 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chains 1, 2, 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, 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 4: Chains 1, 2, 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, 2, 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    
 
 
Nat Struct Biol 4:666-674 (1997)
PubMed id: 9253417  
 
 
Structural studies of poliovirus mutants that overcome receptor defects.
M.W.Wien, S.Curry, D.J.Filman, J.M.Hogle.
 
  ABSTRACT  
 
In order to better understand the process of cell entry for non-enveloped viruses, we have solved the crystal structures of five poliovirus mutants which can infect cells expressing mutant poliovirus receptors. Four of these structures have been solved from frozen crystals using cryocrystallographic data collection methods. The mutations have a range of structural consequences, from small local perturbations to significant loop rearrangements. All of the mutant viruses are more labile to conversion to an apparent cell entry intermediate, suggesting that these mutant viruses could compensate for the suboptimal receptors by lowering the thermal energy required to undergo the receptor-mediated conformational change.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20181687 H.C.Levy, M.Bostina, D.J.Filman, and J.M.Hogle (2010).
Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.
  J Virol, 84, 4426-4441.
PDB codes: 3iyb 3iyc
18559932 B.H.Chua, P.Phuektes, S.A.Sanders, P.K.Nicholls, and P.C.McMinn (2008).
The molecular basis of mouse adaptation by human enterovirus 71.
  J Gen Virol, 89, 1622-1632.  
17827314 E.Dedepsidis, Z.Kyriakopoulou, V.Pliaka, C.Kottaridi, E.Bolanaki, S.Levidiotou-Stefanou, D.Komiotis, and P.Markoulatos (2007).
Retrospective characterization of a vaccine-derived poliovirus type 1 isolate from sewage in Greece.
  Appl Environ Microbiol, 73, 6697-6704.  
17121801 K.J.Koudelka, C.S.Rae, M.J.Gonzalez, and M.Manchester (2007).
Interaction between a 54-kilodalton mammalian cell surface protein and cowpea mosaic virus.
  J Virol, 81, 1632-1640.  
16972033 E.Dedepsidis, I.Karakasiliotis, E.Paximadi, Z.Kyriakopoulou, D.Komiotis, and P.Markoulatos (2006).
Detection of unusual mutation within the VP1 region of different re-isolates of poliovirus Sabin vaccine.
  Virus Genes, 33, 183-191.  
14981262 J.Reguera, A.Carreira, L.Riolobos, J.M.Almendral, and M.G.Mateu (2004).
Role of interfacial amino acid residues in assembly, stability, and conformation of a spherical virus capsid.
  Proc Natl Acad Sci U S A, 101, 2724-2729.  
12142481 J.M.Hogle (2002).
Poliovirus cell entry: common structural themes in viral cell entry pathways.
  Annu Rev Microbiol, 56, 677-702.  
11991962 J.Martín, and P.D.Minor (2002).
Characterization of CHAT and Cox type 1 live-attenuated poliovirus vaccine strains.
  J Virol, 76, 5339-5349.  
12007645 P.C.McMinn (2002).
An overview of the evolution of enterovirus 71 and its clinical and public health significance.
  FEMS Microbiol Rev, 26, 91.  
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.  
10799586 E.V.Grgacic, and H.Schaller (2000).
A metastable form of the large envelope protein of duck hepatitis B virus: low-pH release results in a transition to a hydrophobic, potentially fusogenic conformation.
  J Virol, 74, 5116-5122.  
9631286 J.J.Rux, and R.M.Burnett (1998).
Spherical viruses.
  Curr Opin Struct Biol, 8, 142-149.  
  9573224 Z.Che, N.H.Olson, D.Leippe, W.M.Lee, A.G.Mosser, R.R.Rueckert, T.S.Baker, and T.J.Smith (1998).
Antibody-mediated neutralization of human rhinovirus 14 explored by means of cryoelectron microscopy and X-ray crystallography of virus-Fab complexes.
  J Virol, 72, 4610-4622.
PDB code: 1a6t
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.