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

 

 

 

 

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Contents
Protein chains
273 a.a. *
255 a.a. *
236 a.a. *
40 a.a. *
Ligands
W84
* Residue conservation analysis
PDB id:
1ruh
Name: Virus
Title: Rhinovirus 14 mutant n1219s complexed with antiviral compound win 52084
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. The presence of win compounds win 52035 and 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:
A.T.Hadfield et al. (1995). Structural studies on human rhinovirus 14 drug-resistant compensation mutants. J Mol Biol, 253, 61-73. PubMed id: 7473717 DOI: 10.1006/jmbi.1995.0536
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 from Human rhinovirus 14
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 from Human rhinovirus 14
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 from Human rhinovirus 14
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 from Human rhinovirus 14
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: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
RNA(n)
 + ribonucleoside 5'-triphosphate
 = RNA(n+1)
 + diphosphate
   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: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H+
ribonucleoside 5'-triphosphate
 + H2O
 = ribonucleoside 5'-diphosphate
 + phosphate
 + H(+)
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    
 
 
DOI no: 10.1006/jmbi.1995.0536 J Mol Biol 253:61-73 (1995)
PubMed id: 7473717  
 
 
Structural studies on human rhinovirus 14 drug-resistant compensation mutants.
A.T.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.
 
  ABSTRACT  
 
Structures have been determined of three human rhinovirus 14 (HRV14) compensation mutants that have resistance to the antiviral capsid binding compounds WIN 52035 and WIN 52084. In addition, the structure of HRV14 is reported, with a site-directed mutation at residue 1219 in VP1. A spontaneous mutation occurs at the same site in one of the compensation mutants. Some of the mutations are on the viral surface in the canyon and some lie within the hydrophobic binding pocket in VP1 below the ICAM footprint. Those mutant virus strains with mutations on the surface bind better to cells than does wild-type virus. The antiviral compounds bind to the mutant viruses in a manner similar to their binding to wild-type virus. The receptor and WIN compound binding sites overlap, causing competition between receptor attachment and antiviral compound binding. The compensation mutants probably function by shifting the equilibrium in favor of receptor binding. The mutations in the canyon increase the affinity of the virus for the receptor, while the mutations in the pocket probably decrease the affinity of the WIN compounds for the virus by reducing favorable hydrophobic contacts and constricting the pore through which the antiviral compounds are thought to enter the pocket. This is in contrast to the resistant exclusion mutants that block compounds from binding by increasing the bulk of residues within the hydrophobic pocket in VP1.
 
  Selected figure(s)  
 
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (1995, 253, 61-73) copyright 1995.  
  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.  
  19053243 Z.Zhou, M.Khaliq, J.E.Suk, C.Patkar, L.Li, R.J.Kuhn, and C.B.Post (2008).
Antiviral compounds discovered by virtual screening of small-molecule libraries against dengue virus E protein.
  ACS Chem Biol, 3, 765-775.  
17334823 K.H.Kim (2007).
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?
  J Comput Aided Mol Des, 21, 63-86.  
15883190 L.Wang, and D.L.Smith (2005).
Capsid structure and dynamics of a human rhinovirus probed by hydrogen exchange mass spectrometry.
  Protein Sci, 14, 1661-1672.  
15331736 C.Xiao, T.J.Tuthill, C.M.Bator Kelly, L.J.Challinor, P.R.Chipman, R.A.Killington, D.J.Rowlands, A.Craig, and M.G.Rossmann (2004).
Discrimination among rhinovirus serotypes for a variant ICAM-1 receptor molecule.
  J Virol, 78, 10034-10044.  
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.  
15328120 S.R.Shih, M.C.Tsai, S.N.Tseng, K.F.Won, K.S.Shia, W.T.Li, J.H.Chern, G.W.Chen, C.C.Lee, Y.C.Lee, K.C.Peng, and Y.S.Chao (2004).
Mutation in enterovirus 71 capsid protein VP1 confers resistance to the inhibitory effects of pyridyl imidazolidinone.
  Antimicrob Agents Chemother, 48, 3523-3529.  
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
12110211 M.G.Rossmann, Y.He, and R.J.Kuhn (2002).
Picornavirus-receptor interactions.
  Trends Microbiol, 10, 324-331.  
11159387 B.Speelman, B.R.Brooks, and C.B.Post (2001).
Molecular dynamics simulations of human rhinovirus and an antiviral compound.
  Biophys J, 80, 121-129.  
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.  
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.  
10562537 P.R.Kolatkar, J.Bella, N.H.Olson, C.M.Bator, T.S.Baker, and M.G.Rossmann (1999).
Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor.
  EMBO J, 18, 6249-6259.
PDB codes: 1d3e 1d3i 1d3l
9539703 J.Bella, P.R.Kolatkar, C.W.Marlor, J.M.Greve, and M.G.Rossmann (1998).
The structure of the two amino-terminal domains of human ICAM-1 suggests how it functions as a rhinovirus receptor and as an LFA-1 integrin ligand.
  Proc Natl Acad Sci U S A, 95, 4140-4145.
PDB code: 1iam
9083115 A.T.Hadfield, W.Lee, R.Zhao, M.A.Oliveira, I.Minor, R.R.Rueckert, and M.G.Rossmann (1997).
The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle.
  Structure, 5, 427-441.
PDB code: 1aym
9253417 M.W.Wien, S.Curry, D.J.Filman, and J.M.Hogle (1997).
Structural studies of poliovirus mutants that overcome receptor defects.
  Nat Struct Biol, 4, 666-674.
PDB codes: 1al2 1ar6 1ar7 1ar8 1ar9 1asj
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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