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PDBsum entry 1ruj

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protein Protein-protein interface(s) links
Virus PDB id
1ruj
Jmol
Contents
Protein chains
273 a.a. *
255 a.a. *
236 a.a. *
40 a.a. *
* Residue conservation analysis
PDB id:
1ruj
Name: Virus
Title: Rhinovirus 14 mutant with ser 1 223 replaced by gly (s1223g)
Structure: Rhinovirus 14. Chain: 1. Synonym: hrv14. Engineered: yes. Mutation: yes. Rhinovirus 14. Chain: 2. Synonym: hrv14. Engineered: yes.
Source: Human rhinovirus 14. Organism_taxid: 12131. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hela cells. Other_details: hela cells, mutants found by screening techniques in the presence of win compounds win 52035 and win 52084. Win 52084
Resolution:
3.00Å     R-factor:   not given    
Authors: A.Hadfield,M.A.Oliveira,K.H.Kim,I.Minor,M.J.Kremer, B.A.Heinz,D.Shepard,D.C.Pevear,R.R.Rueckert,M.G.Rossmann
Key ref: D.A.Shepard et al. (1993). WIN 52035-2 inhibits both attachment and eclipse of human rhinovirus 14. J Virol, 67, 2245-2254. PubMed id: 8383239
Date:
09-Jun-95     Release date:   14-Nov-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03303  (POLG_HRV14) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2179 a.a.
273 a.a.*
Protein chain
Pfam   ArchSchema ?
P03303  (POLG_HRV14) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2179 a.a.
255 a.a.*
Protein chain
Pfam   ArchSchema ?
P03303  (POLG_HRV14) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2179 a.a.
236 a.a.
Protein chain
Pfam   ArchSchema ?
P03303  (POLG_HRV14) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2179 a.a.
40 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    
 
 
J Virol 67:2245-2254 (1993)
PubMed id: 8383239  
 
 
WIN 52035-2 inhibits both attachment and eclipse of human rhinovirus 14.
D.A.Shepard, B.A.Heinz, R.R.Rueckert.
 
  ABSTRACT  
 
WIN compounds inhibit attachment of human rhinovirus 14 by binding to a hydrophobic pocket within the capsid and inducing conformational changes in the canyon floor, the region that binds the cellular receptor. To study the basis of drug resistance, we isolated and characterized a family of human rhinovirus 14 mutants resistant to WIN 52035-2. Thermostabilization data and single-cycle growth curves provided evidence for two classes of resistant mutants. One class, here called exclusion mutants, showed a marked decrease in drug-binding affinity and was characterized by substitution to bulkier amino acid side chains at two sites lining the hydrophobic pocket. The other class, called compensation mutants, displayed single-amino-acid substitutions in the drug-deformable regions of the canyon; these mutants were able to attach to cells despite the presence of bound drug. A delay in the rise period of the growth curves of compensation mutants indicated a second locus of drug action. WIN 52035-2 was found to inhibit the first step of uncoating, release of VP4. Attempts to identify this site of drug action by using single-step growth curves were obscured by abortive elution of a major fraction of cell-attached virus. The drug had no effect on the rate of this process but did affect the spectrum of particles produced.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17428846 U.Katpally, and T.J.Smith (2007).
Pocket factors are unlikely to play a major role in the life cycle of human rhinovirus.
  J Virol, 81, 6307-6315.  
16251287 D.C.Pevear, F.G.Hayden, T.M.Demenczuk, L.R.Barone, M.A.McKinlay, and M.S.Collett (2005).
Relationship of pleconaril susceptibility and clinical outcomes in treatment of common colds caused by rhinoviruses.
  Antimicrob Agents Chemother, 49, 4492-4499.  
15016887 R.M.Ledford, N.R.Patel, T.M.Demenczuk, A.Watanyar, T.Herbertz, M.S.Collett, and D.C.Pevear (2004).
VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds.
  J Virol, 78, 3663-3674.  
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
12743280 W.M.Lee, and W.Wang (2003).
Human rhinovirus type 16: mutant V1210A requires capsid-binding drug for assembly of pentamers to form virions during morphogenesis.
  J Virol, 77, 6235-6244.  
10756027 H.Shimizu, M.Agoh, Y.Agoh, H.Yoshida, K.Yoshii, T.Yoneyama, A.Hagiwara, and T.Miyamura (2000).
Mutations in the 2C region of poliovirus responsible for altered sensitivity to benzimidazole derivatives.
  J Virol, 74, 4146-4154.  
  10510336 J.Stöckl, H.Vetr, O.Majdic, G.Zlabinger, E.Kuechler, and W.Knapp (1999).
Human major group rhinoviruses downmodulate the accessory function of monocytes by inducing IL-10.
  J Clin Invest, 104, 957-965.  
  9882307 M.Arita, H.Horie, M.Arita, and A.Nomoto (1999).
Interaction of poliovirus with its receptor affords a high level of infectivity to the virion in poliovirus infections mediated by the Fc receptor.
  J Virol, 73, 1066-1074.  
  9445020 W.Wang, W.M.Lee, A.G.Mosser, and R.R.Rueckert (1998).
WIN 52035-dependent human rhinovirus 16: assembly deficiency caused by mutations near the canyon surface.
  J Virol, 72, 1210-1218.  
  9343235 L.M.Vance, N.Moscufo, M.Chow, and B.A.Heinz (1997).
Poliovirus 2C region functions during encapsidation of viral RNA.
  J Virol, 71, 8759-8765.  
  8940439 B.Lina, M.Valette, S.Foray, J.Luciani, J.Stagnara, D.M.See, and M.Aymard (1996).
Surveillance of community-acquired viral infections due to respiratory viruses in Rhone-Alpes (France) during winter 1994 to 1995.
  J Clin Microbiol, 34, 3007-3011.  
  7769678 B.A.Heinz, and L.M.Vance (1995).
The antiviral compound enviroxime targets the 3A coding region of rhinovirus and poliovirus.
  J Virol, 69, 4189-4197.  
7732663 W.M.Lee, W.Wang, and R.R.Rueckert (1995).
Complete sequence of the RNA genome of human rhinovirus 16, a clinically useful common cold virus belonging to the ICAM-1 receptor group.
  Virus Genes, 9, 177-181.  
  7609025 Z.Tu, N.M.Chapman, G.Hufnagel, S.Tracy, J.R.Romero, W.H.Barry, L.Zhao, K.Currey, and B.Shapiro (1995).
The cardiovirulent phenotype of coxsackievirus B3 is determined at a single site in the genomic 5' nontranslated region.
  J Virol, 69, 4607-4618.  
  7966611 A.G.Mosser, J.Y.Sgro, and R.R.Rueckert (1994).
Distribution of drug resistance mutations in type 3 poliovirus identifies three regions involved in uncoating functions.
  J Virol, 68, 8193-8201.  
  7813425 E.Colston, and V.R.Racaniello (1994).
Soluble receptor-resistant poliovirus mutants identify surface and internal capsid residues that control interaction with the cell receptor.
  EMBO J, 13, 5855-5862.  
  7849588 M.G.Rossmann (1994).
Viral cell recognition and entry.
  Protein Sci, 3, 1712-1725.  
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.