PDBsum entry 1rhi

Go to PDB code: 
protein metals Protein-protein interface(s) links
Virus PDB id
Protein chains
273 a.a. *
255 a.a. *
236 a.a. *
43 a.a. *
* Residue conservation analysis
PDB id:
Name: Virus
Title: Human rhinovirus 3 coat protein
Structure: Human rhinovirus 3 coat protein. Chain: 1. Human rhinovirus 3 coat protein. Chain: 2. Human rhinovirus 3 coat protein. Chain: 3. Human rhinovirus 3 coat protein. Chain: 4
Source: Human rhinovirus 3. Organism_taxid: 44130. Cell_line: hela cell. Cell_line: hela cell
3.00Å     R-factor:   0.284     R-free:   0.288
Authors: R.Zhao,M.G.Rossmann
Key ref:
R.Zhao et al. (1996). Human rhinovirus 3 at 3.0 A resolution. Structure, 4, 1205-1220. PubMed id: 8939746 DOI: 10.1016/S0969-2126(96)00128-1
17-Jun-96     Release date:   12-Mar-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q82081  (POLG_HRV3) -  Genome polyprotein
2178 a.a.
273 a.a.*
Protein chain
Pfam   ArchSchema ?
Q82081  (POLG_HRV3) -  Genome polyprotein
2178 a.a.
255 a.a.*
Protein chain
Pfam   ArchSchema ?
Q82081  (POLG_HRV3) -  Genome polyprotein
2178 a.a.
236 a.a.*
Protein chain
Pfam   ArchSchema ?
Q82081  (POLG_HRV3) -  Genome polyprotein
2178 a.a.
43 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chains 1, 2, 3, 4: E.C.  - 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.  - 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.  - 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.  - Nucleoside-triphosphate phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NTP + H2O = NDP + phosphate
+ H(2)O
+ 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  


DOI no: 10.1016/S0969-2126(96)00128-1 Structure 4:1205-1220 (1996)
PubMed id: 8939746  
Human rhinovirus 3 at 3.0 A resolution.
R.Zhao, D.C.Pevear, M.J.Kremer, V.L.Giranda, J.A.Kofron, R.J.Kuhn, M.G.Rossmann.
BACKGROUND: The over 100 serotypes of human rhinoviruses (HRV) are major causative agents of the common cold in humans. These HRVs can be roughly divided into a major and minor group according to their cellular receptors. They can also be divided into two antiviral groups, A and B, based on their sensitivity to different capsid-binding antiviral compounds. The crystal structures of HRV14 and HRV16, major-receptor group rhinoviruses, as well as HRV1A, a minor-receptor group rhinovirus, were determined previously. Sequence comparisons had shown that HRV14 seemed to be an outlier among rhinoviruses. Furthermore, HRV14 was the only virus with no cellular 'pocket factor' in a hydrophobic pocket which is targeted by many capsid-binding antiviral compounds and is thought to regulate viral stability. HRV3, another major-receptor group virus, was chosen for study because it is one of a subset of serotypes that best represents the drug sensitivity of most rhinovirus serotypes. Both HRV3 and HRV14 belong to antiviral group A, while HRV16 and HRV1A belong to antiviral group B. RESULTS: HRV3 was found to be very similar to HRV14 in sequence and structure. Like HRV14, crystallized HRV3 also has no bound pocket factor. The structure of HRV3 complexed with an antiviral compound, WIN56291, was also determined and found to be similar to the same antiviral compound complexed with HRV14. CONCLUSIONS: The amino-acid sequence and structural similarity between HRV3 and HRV14 suggests that rhinoviruses in the same antiviral group have similar amino-acid sequences and structures. The similar amino-acid composition in the pocket region and the viral protein VP1 N termini in all known group B HRV sequences suggests that these viruses may all contain pocket factors and ordered N-terminal amphipathic helices in VP1. Both of these factors contribute to viral stability, which is consistent with the observations that group B rhinoviruses have a higher chance of successful transmission from one host to another and is a possible explanation for the observed higher pathogenicity of these rhinoviruses.
  Selected figure(s)  
Figure 1.
Figure 1. Diagrammatic view of picornavirus with enlargement of one icosahedral asymmetric unit showing the outline of the canyon and the entrance to the antiviral-binding pocket. The protomeric assembly unit (which differs from the geometric definition of the asymmetric unit) is shown in heavy outline on the icosahedron. The arrow B shows the direction of view used in Figure 7. (The figure was adapted from Oliveira et al. [7], with permission.)
  The above figure is reprinted by permission from Cell Press: Structure (1996, 4, 1205-1220) copyright 1996.  
  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.  
19714577 J.M.Rollinger, and M.Schmidtke (2011).
The human rhinovirus: human-pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery.
  Med Res Rev, 31, 42-92.  
21483405 Y.A.Bochkov, A.C.Palmenberg, W.M.Lee, J.A.Rathe, S.P.Amineva, X.Sun, T.R.Pasic, N.N.Jarjour, S.B.Liggett, and J.E.Gern (2011).
Molecular modeling, organ culture and reverse genetics for a newly identified human rhinovirus C.
  Nat Med, 17, 627-632.  
20404439 A.Janner (2010).
Form, symmetry and packing of biomacromolecules. II. Serotypes of human rhinovirus.
  Acta Crystallogr A, 66, 312-326.  
19403680 U.Katpally, T.M.Fu, D.C.Freed, D.R.Casimiro, and T.J.Smith (2009).
Antibodies to the buried N terminus of rhinovirus VP4 exhibit cross-serotypic neutralization.
  J Virol, 83, 7040-7048.  
18256154 M.P.Davis, G.Bottley, L.P.Beales, R.A.Killington, D.J.Rowlands, and T.J.Tuthill (2008).
Recombinant VP4 of human rhinovirus induces permeability in model membranes.
  J Virol, 82, 4169-4174.  
18499644 S.T.Pruett, A.Bushnev, K.Hagedorn, M.Adiga, C.A.Haynes, M.C.Sullards, D.C.Liotta, and A.H.Merrill (2008).
Biodiversity of sphingoid bases ("sphingosines") and related amino alcohols.
  J Lipid Res, 49, 1621-1639.  
18940610 S.Venkataraman, S.P.Reddy, J.Loo, N.Idamakanti, P.L.Hallenbeck, and V.S.Reddy (2008).
Structure of Seneca Valley Virus-001: an oncolytic picornavirus representing a new genus.
  Structure, 16, 1555-1561.
PDB code: 3cji
17927830 D.Zhu, G.E.Fox, and S.Chakravarty (2007).
RECOVIR: an application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses.
  BMC Bioinformatics, 8, 379.  
15994818 X.Yan, P.R.Chipman, T.Castberg, G.Bratbak, and T.S.Baker (2005).
The marine algal virus PpV01 has an icosahedral capsid with T=219 quasisymmetry.
  J Virol, 79, 9236-9243.  
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.  
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
12743267 L.Xing, J.M.Casasnovas, and R.H.Cheng (2003).
Structural analysis of human rhinovirus complexed with ICAM-1 reveals the dynamics of receptor-mediated virus uncoating.
  J Virol, 77, 6101-6107.  
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
12121655 J.Ding, A.D.Smith, S.C.Geisler, X.Ma, G.F.Arnold, and E.Arnold (2002).
Crystal structure of a human rhinovirus that displays part of the HIV-1 V3 loop and induces neutralizing antibodies against HIV-1.
  Structure, 10, 999.
PDB code: 1k5m
12142481 J.M.Hogle (2002).
Poliovirus cell entry: common structural themes in viral cell entry pathways.
  Annu Rev Microbiol, 56, 677-702.  
12072496 M.Reithmayer, A.Reischl, L.Snyers, and D.Blaas (2002).
Species-specific receptor recognition by a minor-group human rhinovirus (HRV): HRV serotype 1A distinguishes between the murine and the human low-density lipoprotein receptor.
  J Virol, 76, 6957-6965.  
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.  
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.  
10838576 J.M.Casasnovas (2000).
The dynamics of receptor recognition by human rhinoviruses.
  Trends Microbiol, 8, 251-254.  
10716921 L.Xing, K.Tjarnlund, B.Lindqvist, G.G.Kaplan, D.Feigelstock, R.H.Cheng, and J.M.Casasnovas (2000).
Distinct cellular receptor interactions in poliovirus and rhinoviruses.
  EMBO J, 19, 1207-1216.  
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
10417415 N.Verdaguer, T.C.Marlovits, J.Bravo, D.I.Stuart, D.Blaas, and I.Fita (1999).
Crystallization and preliminary X-ray analysis of human rhinovirus serotype 2 (HRV2).
  Acta Crystallogr D Biol Crystallogr, 55, 1459-1461.  
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
  9557730 E.A.Hewat, T.C.Marlovits, and D.Blaas (1998).
Structure of a neutralizing antibody bound monovalently to human rhinovirus 2.
  J Virol, 72, 4396-4402.  
9631286 J.J.Rux, and R.M.Burnett (1998).
Spherical viruses.
  Curr Opin Struct Biol, 8, 142-149.  
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
9345628 K.Moffat, and Z.Ren (1997).
Synchrotron radiation applications to macromolecular crystallography.
  Curr Opin Struct Biol, 7, 689-696.  
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
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 code is shown on the right.