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PDBsum entry 1vbb
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Virus PDB id
1vbb

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
279 a.a. *
266 a.a. *
235 a.a. *
62 a.a. *
Ligands
ILE-SER-GLU-VAL
J80
MYR
* Residue conservation analysis
PDB id:
1vbb
Name: Virus
Title: Poliovirus (type 3, sabin strain) (p3/sabin, p3/leon/12a(1)b) complexed with r80633
Structure: Poliovirus type 3. Chain: 0. Poliovirus type 3. Chain: 1. Other_details: the numbering of the vp1 residues has been altered to facilitate comparison with the structure of the mahoney strain of type 1 poliovirus (PDB entry 2plv). Mahoney has a two residue insertion, relative to p3/sabin, located in the disordered n-terminus of vp1. Thus the residues numbered 24 - 302 in this entry are
Source: Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b). Organism_taxid: 12088. Strain: p3-sabin. Other_details: p3/sabin prepared from a low-passage seed stock of a plaque isolate (p3/leon/12a(1)b placque 411) obtained from p.D.Minor (national institute for biological standards control, london). Organ: seed. (National institute for biological standards control, london)
Resolution:
2.80Å     R-factor:   0.278    
Authors: R.A.Grant,C.N.Hiremath,D.J.Filman,R.Syed,K.Andries,J.M.Hogle
Key ref: R.A.Grant et al. (1994). Structures of poliovirus complexes with anti-viral drugs: implications for viral stability and drug design. Curr Biol, 4, 784-797. PubMed id: 7820548
Date:
02-Jan-96     Release date:   11-Jul-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03302  (POLG_POL3L) -  Genome polyprotein from Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2206 a.a.
279 a.a.*
Protein chain
Pfam   ArchSchema ?
P03302  (POLG_POL3L) -  Genome polyprotein from Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2206 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P03302  (POLG_POL3L) -  Genome polyprotein from Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2206 a.a.
235 a.a.*
Protein chain
Pfam   ArchSchema ?
P03302  (POLG_POL3L) -  Genome polyprotein from Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2206 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 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    
 
 
Curr Biol 4:784-797 (1994)
PubMed id: 7820548  
 
 
Structures of poliovirus complexes with anti-viral drugs: implications for viral stability and drug design.
R.A.Grant, C.N.Hiremath, D.J.Filman, R.Syed, K.Andries, J.M.Hogle.
 
  ABSTRACT  
 
BACKGROUND: Picornaviruses, such as the structurally related polioviruses and rhinoviruses, are important human pathogens which have been the target of major drug development efforts. Receptor-mediated uncoating and thermal inactivation of poliovirus and rhinovirus are inhibited by agents that bind to each virus by inserting into a pocket in the beta barrel of the viral capsid protein, VP1. This pocket, which is normally empty in human rhinovirus-14 (HRV14), is occupied by an unknown natural ligand in poliovirus. Structural studies of HRV14-drug complexes have shown that drug binding causes large, localized changes in the conformation of VP1. RESULTS: We report the crystal structures of six complexes between poliovirus and capsid-binding, antiviral drugs, including complexes of four different drugs with the Sabin vaccine strain of type 3 poliovirus, and complexes of one of these drugs with two other poliovirus strains that contain sequence differences in the drug-binding site. In each complex, the changes in capsid structure associated with drug binding are limited to minor adjustments in the conformations of a few side chains lining the binding site. CONCLUSIONS: The minor structural changes caused by drug binding suggest a model of drug action in which it is the conformational changes prevented by the bound drug, rather than obvious conformational changes induced by drug binding, which exert the biological effect. Our results, along with additional structures of rhinovirus-drug complexes, suggest possible improvements in drug design, and provide important clues about the nature of the conformational changes that are involved in the uncoating process.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22472617 J.M.Hogle (2012).
A 3D framework for understanding enterovirus 71.
  Nat Struct Mol Biol, 19, 367-368.  
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
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
  20397067 T.J.Tuthill, E.Groppelli, J.M.Hogle, and D.J.Rowlands (2010).
Picornaviruses.
  Curr Top Microbiol Immunol, 343, 43-89.  
18328076 E.Dedepsidis, V.Pliaka, Z.Kyriakopoulou, C.Brakoulias, S.Levidiotou-Stefanou, A.Pratti, Z.Mamuris, and P.Markoulatos (2008).
Complete genomic characterization of an intertypic Sabin 3/Sabin 2 capsid recombinant.
  FEMS Immunol Med Microbiol, 52, 343-351.  
  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.  
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.  
17006877 S.J.Stray, and A.Zlotnick (2006).
BAY 41-4109 has multiple effects on Hepatitis B virus capsid assembly.
  J Mol Recognit, 19, 542-548.  
16251182 J.Zhou, L.Huang, D.L.Hachey, C.H.Chen, and C.Aiken (2005).
Inhibition of HIV-1 maturation via drug association with the viral Gag protein in immature HIV-1 particles.
  J Biol Chem, 280, 42149-42155.  
15899980 Y.Li, Z.Zhou, and C.B.Post (2005).
Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid.
  Proc Natl Acad Sci U S A, 102, 7529-7534.  
15155227 A.L.Salvati, A.De Dominicis, S.Tait, A.Canitano, A.Lahm, and L.Fiore (2004).
Mechanism of action at the molecular level of the antiviral drug 3(2H)-isoflavene against type 2 poliovirus.
  Antimicrob Agents Chemother, 48, 2233-2243.  
15349956 R.K.Evans, D.K.Nawrocki, L.A.Isopi, D.M.Williams, D.R.Casimiro, S.Chin, M.Chen, D.M.Zhu, J.W.Shiver, and D.B.Volkin (2004).
Development of stable liquid formulations for adenovirus-based vaccines.
  J Pharm Sci, 93, 2458-2475.  
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
12941886 N.Verdaguer, M.A.Jimenez-Clavero, I.Fita, and V.Ley (2003).
Structure of swine vesicular disease virus: mapping of changes occurring during adaptation of human coxsackie B5 virus to infect swine.
  J Virol, 77, 9780-9789.
PDB code: 1mqt
12142481 J.M.Hogle (2002).
Poliovirus cell entry: common structural themes in viral cell entry pathways.
  Annu Rev Microbiol, 56, 677-702.  
12384371 S.Höglund, J.Su, S.S.Reneby, A.Végvári, S.Hjertén, I.M.Sintorn, H.Foster, Y.P.Wu, I.Nyström, and A.Vahlne (2002).
Tripeptide interference with human immunodeficiency virus type 1 morphogenesis.
  Antimicrob Agents Chemother, 46, 3597-3605.  
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.  
11134318 M.A.Jiménez-Clavero, E.Escribano-Romero, A.J.Douglas, and V.Ley (2001).
The N-terminal region of the VP1 protein of swine vesicular disease virus contains a neutralization site that arises upon cell attachment and is involved in viral entry.
  J Virol, 75, 1044-1047.  
11333877 S.K.Tsang, B.M.McDermott, V.R.Racaniello, and J.M.Hogle (2001).
Kinetic analysis of the effect of poliovirus receptor on viral uncoating: the receptor as a catalyst.
  J Virol, 75, 4984-4989.  
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.  
10729171 A.W.Dove, and V.R.Racaniello (2000).
An antiviral compound that blocks structural transitions of poliovirus prevents receptor binding at low temperatures.
  J Virol, 74, 3929-3931.  
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.  
10611281 A.T.Hadfield, G.D.Diana, and M.G.Rossmann (1999).
Analysis of three structurally related antiviral compounds in complex with human rhinovirus 16.
  Proc Natl Acad Sci U S A, 96, 14730-14735.
PDB codes: 1qju 1qjx 1qjy
  10595531 D.K.Phelps, and C.B.Post (1999).
Molecular dynamics investigation of the effect of an antiviral compound on human rhinovirus.
  Protein Sci, 8, 2281-2289.  
10647183 E.Hendry, H.Hatanaka, E.Fry, M.Smyth, J.Tate, G.Stanway, J.Santti, M.Maaronen, T.Hyypiä, and D.Stuart (1999).
The crystal structure of coxsackievirus A9: new insights into the uncoating mechanisms of enteroviruses.
  Structure, 7, 1527-1538.
PDB code: 1d4m
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
9294865 D.Joseph-McCarthy, J.M.Hogle, and M.Karplus (1997).
Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs.
  Proteins, 29, 32-58.  
9413981 D.S.Dimitrov (1997).
How do viruses enter cells? The HIV coreceptors teach us a lesson of complexity.
  Cell, 91, 721-730.  
9261087 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, and E.Arnold (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.
PDB code: 1eah
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
  8995703 W.Kraus, H.Zimmermann, H.J.Eggers, and B.Nelsen-Salz (1997).
Rhodanine resistance and dependence of echovirus 12: a possible consequence of capsid flexibility.
  J Virol, 71, 1697-1702.  
8805560 M.W.Wien, M.Chow, and J.M.Hogle (1996).
Poliovirus: new insights from an old paradigm.
  Structure, 4, 763-767.  
  7609049 E.M.Colston, and V.R.Racaniello (1995).
Poliovirus variants selected on mutant receptor-expressing cells identify capsid residues that expand receptor recognition.
  J Virol, 69, 4823-4829.  
8591043 J.K.Muckelbauer, M.Kremer, I.Minor, G.Diana, F.J.Dutko, J.Groarke, D.C.Pevear, and M.G.Rossmann (1995).
The structure of coxsackievirus B3 at 3.5 A resolution.
  Structure, 3, 653-667.  
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
  7849583 R.Basavappa, R.Syed, O.Flore, J.P.Icenogle, D.J.Filman, and J.M.Hogle (1994).
Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 A resolution.
  Protein Sci, 3, 1651-1669.
PDB code: 1pov
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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