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PDBsum entry 1pov

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protein ligands Protein-protein interface(s) links
Virus PDB id
1pov
Jmol
Contents
Protein chains
300 a.a. *
235 a.a. *
238 a.a. *
Ligands
MYR
SPH
Waters ×210
* Residue conservation analysis
PDB id:
1pov
Name: Virus
Title: Role and mechanism of the maturation cleavage of vp0 in poli assembly: structure of the empty capsid assembly intermedia angstroms resolution
Structure: Poliovirus native empty capsid (type 1). Chain: 0. Poliovirus native empty capsid (type 1). Chain: 1. Poliovirus native empty capsid (type 1). Chain: 3
Source: Human poliovirus 1. Organism_taxid: 12081. Strain: mahoney. Strain: mahoney
Resolution:
2.80Å     R-factor:   0.281    
Authors: R.Basavappa,D.J.Filman,J.M.Hogle
Key ref: R.Basavappa et al. (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. PubMed id: 7849583 DOI: 10.1002/pro.5560031005
Date:
10-Aug-95     Release date:   07-Dec-95    
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.
300 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.
238 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: Chains 0, 1, 3: 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 0, 1, 3: 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 0, 1, 3: 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 0, 1, 3: 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: 10.1002/pro.5560031005 Protein Sci 3:1651-1669 (1994)
PubMed id: 7849583  
 
 
Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 A resolution.
R.Basavappa, R.Syed, O.Flore, J.P.Icenogle, D.J.Filman, J.M.Hogle.
 
  ABSTRACT  
 
The crystal structure of the P1/Mahoney poliovirus empty capsid has been determined at 2.9 A resolution. The empty capsids differ from mature virions in that they lack the viral RNA and have yet to undergo a stabilizing maturation cleavage of VP0 to yield the mature capsid proteins VP4 and VP2. The outer surface and the bulk of the protein shell are very similar to those of the mature virion. The major differences between the 2 structures are focused in a network formed by the N-terminal extensions of the capsid proteins on the inner surface of the shell. In the empty capsids, the entire N-terminal extension of VP1, as well as portions corresponding to VP4 and the N-terminal extension of VP2, are disordered, and many stabilizing interactions that are present in the mature virion are missing. In the empty capsid, the VP0 scissile bond is located some 20 A away from the positions in the mature virion of the termini generated by VP0 cleavage. The scissile bond is located on the rim of a trefoil-shaped depression in the inner surface of the shell that is highly reminiscent of an RNA binding site in bean pod mottle virus. The structure suggests plausible (and ultimately testable) models for the initiation of encapsidation, for the RNA-dependent autocatalytic cleavage of VP0, and for the role of the cleavage in establishing the ordered N-terminal network and in generating stable virions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19710148 S.Goodwin, T.J.Tuthill, A.Arias, R.A.Killington, and D.J.Rowlands (2009).
Foot-and-mouth disease virus assembly: processing of recombinant capsid precursor by exogenous protease induces self-assembly of pentamers in vitro in a myristoylation-dependent manner.
  J Virol, 83, 11275-11282.  
17234885 R.Geller, M.Vignuzzi, R.Andino, and J.Frydman (2007).
Evolutionary constraints on chaperone-mediated folding provide an antiviral approach refractory to development of drug resistance.
  Genes Dev, 21, 195-205.  
16641291 G.Lanzi, J.R.de Miranda, M.B.Boniotti, C.E.Cameron, A.Lavazza, L.Capucci, S.M.Camazine, and C.Rossi (2006).
Molecular and biological characterization of deformed wing virus of honeybees (Apis mellifera L.).
  J Virol, 80, 4998-5009.  
15858032 C.Carrillo, E.R.Tulman, G.Delhon, Z.Lu, A.Carreno, A.Vagnozzi, G.F.Kutish, and D.L.Rock (2005).
Comparative genomics of foot-and-mouth disease virus.
  J Virol, 79, 6487-6504.  
15681401 C.M.Wiethoff, H.Wodrich, L.Gerace, and G.R.Nemerow (2005).
Adenovirus protein VI mediates membrane disruption following capsid disassembly.
  J Virol, 79, 1992-2000.  
15919927 D.Bubeck, D.J.Filman, N.Cheng, A.C.Steven, J.M.Hogle, and D.M.Belnap (2005).
The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes.
  J Virol, 79, 7745-7755.
PDB code: 1xyr
  16300678 D.Franco, H.B.Pathak, C.E.Cameron, B.Rombaut, E.Wimmer, and A.V.Paul (2005).
Stimulation of poliovirus RNA synthesis and virus maturation in a HeLa cell-free in vitro translation-RNA replication system by viral protein 3CDpro.
  Virol J, 2, 86.  
16085909 Y.J.Ko, K.S.Choi, J.J.Nah, D.J.Paton, J.K.Oem, G.Wilsden, S.Y.Kang, N.I.Jo, J.H.Lee, J.H.Kim, H.W.Lee, and J.M.Park (2005).
Noninfectious virus-like particle antigen for detection of swine vesicular disease virus antibodies in pigs by enzyme-linked immunosorbent assay.
  Clin Diagn Lab Immunol, 12, 922-929.  
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.  
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.  
15331714 G.Sánchez, L.Aragonès, M.I.Costafreda, E.Ribes, A.Bosch, and R.M.Pintó (2004).
Capsid region involved in hepatitis A virus binding to glycophorin A of the erythrocyte membrane.
  J Virol, 78, 9807-9813.  
15084510 M.J.Grubman, and B.Baxt (2004).
Foot-and-mouth disease.
  Clin Microbiol Rev, 17, 465-493.  
12692228 P.Danthi, M.Tosteson, Q.H.Li, and M.Chow (2003).
Genome delivery and ion channel properties are altered in VP4 mutants of poliovirus.
  J Virol, 77, 5266-5274.  
12124301 D.Endres, and A.Zlotnick (2002).
Model-based analysis of assembly kinetics for virus capsids or other spherical polymers.
  Biophys J, 83, 1217-1230.  
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.  
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.  
  9847348 C.I.Nugent, K.L.Johnson, P.Sarnow, and K.Kirkegaard (1999).
Functional coupling between replication and packaging of poliovirus replicon RNA.
  J Virol, 73, 427-435.  
  10516013 M.Hindiyeh, Q.H.Li, R.Basavappa, J.M.Hogle, and M.Chow (1999).
Poliovirus mutants at histidine 195 of VP2 do not cleave VP0 into VP2 and VP4.
  J Virol, 73, 9072-9079.  
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
  9696852 R.Basavappa, A.Gómez-Yafal, and J.M.Hogle (1998).
The poliovirus empty capsid specifically recognizes the poliovirus receptor and undergoes some, but not all, of the transitions associated with cell entry.
  J Virol, 72, 7551-7556.  
9519407 V.Chandrasekar, and J.E.Johnson (1998).
The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily.
  Structure, 6, 157-171.
PDB code: 1a6c
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.  
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
  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.  
  9371640 S.Curry, E.Fry, W.Blakemore, R.Abu-Ghazaleh, T.Jackson, A.King, S.Lea, J.Newman, and D.Stuart (1997).
Dissecting the roles of VP0 cleavage and RNA packaging in picornavirus capsid stabilization: the structure of empty capsids of foot-and-mouth disease virus.
  J Virol, 71, 9743-9752.  
  9060641 T.Knipe, E.Rieder, B.Baxt, G.Ward, and P.W.Mason (1997).
Characterization of synthetic foot-and-mouth disease virus provirions separates acid-mediated disassembly from infectivity.
  J Virol, 71, 2851-2856.  
  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.  
  8931139 N.Blom, J.Hansen, D.Blaas, and S.Brunak (1996).
Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks.
  Protein Sci, 5, 2203-2216.  
  8794359 S.Curry, M.Chow, and J.M.Hogle (1996).
The poliovirus 135S particle is infectious.
  J Virol, 70, 7125-7131.  
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.  
7648316 S.C.Harrison (1995).
Virus structures and conformational rearrangements.
  Curr Opin Struct Biol, 5, 157-164.  
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.