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PDBsum entry 1d4m

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protein ligands Protein-protein interface(s) links
Virus PDB id
1d4m
Jmol
Contents
Protein chains
284 a.a. *
252 a.a. *
238 a.a. *
61 a.a. *
Ligands
MYR
W71 ×2
Waters ×448
* Residue conservation analysis
PDB id:
1d4m
Name: Virus
Title: The crystal structure of coxsackievirus a9 to 2.9 a resolution
Structure: Protein (coxsackievirus a9). Chain: 1. Fragment: vp1. Protein (coxsackievirus a9). Chain: 2. Fragment: vp2. Protein (coxsackievirus a9). Chain: 3. Fragment: vp3.
Source: Human coxsackievirus a9. Organism_taxid: 12067. Organism_taxid: 12067
Resolution:
2.90Å     R-factor:   0.169    
Authors: E.Hendry,H.Hatanaka,E.Fry,M.Smyth,J.Tate,G.Stanway,J.Santti, M.Maaronen,T.Hyypia,D.Stuart
Key ref:
E.Hendry et al. (1999). The crystal structure of coxsackievirus A9: new insights into the uncoating mechanisms of enteroviruses. Structure, 7, 1527-1538. PubMed id: 10647183 DOI: 10.1016/S0969-2126(00)88343-4
Date:
04-Oct-99     Release date:   23-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21404  (POLG_CXA9) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2201 a.a.
284 a.a.*
Protein chain
Pfam   ArchSchema ?
P21404  (POLG_CXA9) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2201 a.a.
252 a.a.*
Protein chain
Pfam   ArchSchema ?
P21404  (POLG_CXA9) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2201 a.a.
238 a.a.
Protein chain
Pfam   ArchSchema ?
P21404  (POLG_CXA9) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2201 a.a.
61 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral capsid   1 term 
  Biochemical function     structural molecule activity     1 term  

 

 
DOI no: 10.1016/S0969-2126(00)88343-4 Structure 7:1527-1538 (1999)
PubMed id: 10647183  
 
 
The crystal structure of coxsackievirus A9: new insights into the uncoating mechanisms of enteroviruses.
E.Hendry, H.Hatanaka, E.Fry, M.Smyth, J.Tate, G.Stanway, J.Santti, M.Maaronen, T.Hyypiä, D.Stuart.
 
  ABSTRACT  
 
BACKGROUND: Coxsackievirus A9 (CAV9), a human pathogen causing symptoms ranging from common colds to fatal infections of the central nervous system, is an icosahedral single-stranded RNA virus that belongs to the genus Enterovirus of the family Picornaviridae. One of the four capsid proteins, VP1, includes the arginine-glycine-aspartate (RGD) motif within its C-terminal extension. This region binds to integrin alpha v beta 3, the only receptor for CAV9 to be conclusively identified to date. RESULTS: The crystal structure of CAV9 in complex with the antiviral compound WIN 51711 has been solved to 2.9 A resolution. The structures of the four capsid proteins, VP1 to VP4, resemble those of other picornaviruses. The antiviral compound is bound in the VP1 hydrophobic pocket, and it is possible that the pocket entrance contains a second WIN 51711 molecule. Continuous electron density for the VP1 N terminus provides a complete picture of the structure close to the fivefold axis. The VP1 C-terminal portion is on the outer surface of the virus and becomes disordered five-residues N-terminal to the RGD motif. CONCLUSIONS: The RGD motif is exposed and flexible in common with other known integrin ligands. Although CAV9 resembles coxsackie B viruses (CBVs), several substitutions in the areas implicated in CBV receptor attachment suggest it may recognise a different receptor. The structure along the fivefold axis provides new information on the uncoating mechanism of enteroviruses. CAV9 might bind a larger natural pocket factor than other picornaviruses, an observation of particular relevance to the design of new antiviral compounds.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. The vicinity of the fivefold axis. (a) A close-up of one myristoyl group, shown as a ball-and-stick model, and a portion of the 2F[o]-F[c] electron-density map contoured at 1s. Other myristoyl groups are shown as sticks. Protein subunit backbones are depicted as in Figure 6. Residues and water molecules within 4 of the myristoyl molecules are shown as stick models and spheres, respectively. Schematic representations of (b) CAV9 and (c) HRV16. The fivefold axis runs vertically through the centre of each figure. Two copies of VP1, WIN compounds and pocket factor (labelled PF), five copies each of VP1, VP3 and VP4 N-terminal strands, one copy of the VP3 N-terminal loop, and fivefold axis related putative ions are shown. Residues close to ions are also shown in ball-and-stick representation with atoms in standard colours. (d) Stereoview detailed structure of CAV9 viewed from the centre of the virion. The backbone and sidechain atoms are shown as thick and thin sticks, respectively. The residue number subscript defines the viral protein (e.g. 28[4] is residue 28 of VP4). Figure generated using BOBSCRIPT [52 and 53] and Raster3D [54].
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1527-1538) copyright 1999.  
  Figure was selected by an automated 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
20554778 J.Seitsonen, P.Susi, O.Heikkilä, R.S.Sinkovits, P.Laurinmäki, T.Hyypiä, and S.J.Butcher (2010).
Interaction of alphaVbeta3 and alphaVbeta6 integrins with human parechovirus 1.
  J Virol, 84, 8509-8519.  
20089652 O.Heikkilä, P.Susi, T.Tevaluoto, H.Härmä, V.Marjomäki, T.Hyypiä, and S.Kiljunen (2010).
Internalization of coxsackievirus A9 is mediated by {beta}2-microglobulin, dynamin, and Arf6 but not by caveolin-1 or clathrin.
  J Virol, 84, 3666-3681.  
  20397067 T.J.Tuthill, E.Groppelli, J.M.Hogle, and D.J.Rowlands (2010).
Picornaviruses.
  Curr Top Microbiol Immunol, 343, 43-89.  
17988871 P.L.Stewart, and G.R.Nemerow (2007).
Cell integrins: commonly used receptors for diverse viral pathogens.
  Trends Microbiol, 15, 500-507.  
16455897 C.H.Williams, S.Oikarinen, S.Tauriainen, K.Salminen, H.Hyöty, and G.Stanway (2006).
Molecular analysis of an echovirus 3 strain isolated from an individual concurrently with appearance of islet cell and IA-2 autoantibodies.
  J Clin Microbiol, 44, 441-448.  
16868986 Y.Y.Ke, Y.C.Chen, and T.H.Lin (2006).
Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies.
  J Comput Chem, 27, 1556-1570.  
15194773 C.H.Williams, T.Kajander, T.Hyypiä, T.Jackson, D.Sheppard, and G.Stanway (2004).
Integrin alpha v beta 6 is an RGD-dependent receptor for coxsackievirus A9.
  J Virol, 78, 6967-6973.  
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.  
14701832 L.Xing, M.Huhtala, V.Pietiäinen, J.Käpylä, K.Vuorinen, V.Marjomäki, J.Heino, M.S.Johnson, T.Hyypiä, and R.H.Cheng (2004).
Structural and functional analysis of integrin alpha2I domain interaction with echovirus 1.
  J Biol Chem, 279, 11632-11638.  
15006797 M.Chambon, C.Archimbaud, J.L.Bailly, J.M.Gourgand, F.Charbonné, and H.Peigue-Lafeuille (2004).
Virucidal efficacy of glutaraldehyde against enteroviruses is related to the location of lysine residues in exposed structures of the VP1 capsid protein.
  Appl Environ Microbiol, 70, 1717-1722.  
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
12692248 E.E.Fry, N.J.Knowles, J.W.Newman, G.Wilsden, Z.Rao, A.M.King, and D.I.Stuart (2003).
Crystal structure of Swine vesicular disease virus and implications for host adaptation.
  J Virol, 77, 5475-5486.
PDB code: 1oop
12663789 Y.He, S.Mueller, P.R.Chipman, C.M.Bator, X.Peng, V.D.Bowman, S.Mukhopadhyay, E.Wimmer, R.J.Kuhn, and M.G.Rossmann (2003).
Complexes of poliovirus serotypes with their common cellular receptor, CD155.
  J Virol, 77, 4827-4835.
PDB code: 1nn8
12142481 J.M.Hogle (2002).
Poliovirus cell entry: common structural themes in viral cell entry pathways.
  Annu Rev Microbiol, 56, 677-702.  
12147709 M.S.Smyth, and J.H.Martin (2002).
Picornavirus uncoating.
  Mol Pathol, 55, 214-219.  
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.  
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.  
11178348 J.R.Romero (2001).
Pleconaril: a novel antipicornaviral drug.
  Expert Opin Investig Drugs, 10, 369-379.  
11356285 R.Grabherr, W.Ernst, C.Oker-Blom, and I.Jones (2001).
Developments in the use of baculoviruses for the surface display of complex eukaryotic proteins.
  Trends Biotechnol, 19, 231-236.  
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.