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PDBsum entry 3dpr

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protein ligands metals Protein-protein interface(s) links
Virus PDB id
3dpr
Jmol
Contents
Protein chains
269 a.a. *
250 a.a. *
237 a.a. *
25 a.a. *
39 a.a. *
Ligands
DAO
Metals
_CA
* Residue conservation analysis
PDB id:
3dpr
Name: Virus
Title: Human rhinovirus 2 bound to a concatamer of the vldl recepto v3
Structure: Protein vp1. Chain: a. Synonym: virion protein 1, p1d, coat protein vp1. Protein vp2. Chain: b. Synonym: virion protein 2, p1b, coat protein vp2. Protein vp3. Chain: c. Synonym: virion protein 3, p1c, coat protein vp3.
Source: Human rhinovirus 2. Hrv-2. Organism_taxid: 12130. Strain: human. Other_details: hela cells. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli.
Resolution:
3.50Å     R-factor:   0.426     R-free:   0.441
Authors: J.Querol-Audi,J.Pous,I.Fita,N.Verdaguer
Key ref: J.Querol-Audí et al. (2009). Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition. FEBS Lett, 583, 235-240. PubMed id: 19073182
Date:
09-Jul-08     Release date:   07-Apr-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04936  (POLG_HRV2) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2150 a.a.
269 a.a.
Protein chain
Pfam   ArchSchema ?
P04936  (POLG_HRV2) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2150 a.a.
250 a.a.
Protein chain
Pfam   ArchSchema ?
P04936  (POLG_HRV2) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2150 a.a.
237 a.a.
Protein chain
Pfam   ArchSchema ?
P04936  (POLG_HRV2) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2150 a.a.
25 a.a.*
Protein chain
Pfam   ArchSchema ?
P98155  (VLDLR_HUMAN) -  Very low-density lipoprotein receptor
Seq:
Struc:
 
Seq:
Struc:
873 a.a.
39 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chains A, B, C, D: 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 2: Chains A, B, C, D: 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 3: Chains A, B, C, D: 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 4: Chains A, B, C, D: 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    
 
 
FEBS Lett 583:235-240 (2009)
PubMed id: 19073182  
 
 
Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition.
J.Querol-Audí, T.Konecsni, J.Pous, O.Carugo, I.Fita, N.Verdaguer, D.Blaas.
 
  ABSTRACT  
 
X-ray structures of human rhinovirus 2 (HRV2) in complex with soluble very-low-density lipoprotein receptors encompassing modules 1, 2, and 3 (V123) and five V3 modules arranged in tandem (V33333) demonstrates multi-modular binding around the virion's five-fold axes. Occupancy was 60% for V123 and 100% for V33333 explaining the high-avidity of the interaction. Surface potentials of 3D-models of all minor group HRVs and K-type major group HRVs were compared; hydrophobic interactions between a conserved lysine in the viruses and a tryptophan in the receptor modules together with coulombic attraction via diffuse opposite surface potentials determine minor group HRV receptor specificity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20629045 R.Fuchs, and D.Blaas (2010).
Uncoating of human rhinoviruses.
  Rev Med Virol, 20, 281-297.  
  20397067 T.J.Tuthill, E.Groppelli, J.M.Hogle, and D.J.Rowlands (2010).
Picornaviruses.
  Curr Top Microbiol Immunol, 343, 43-89.  
19676115 D.Beglov, C.J.Lee, A.De Biasio, D.Kozakov, R.Brenke, S.Vajda, and N.Beglova (2009).
Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.
  Proteins, 77, 940-949.  
19706701 T.Konecsni, U.Berka, A.Pickl-Herk, G.Bilek, A.G.Khan, L.Gajdzig, R.Fuchs, and D.Blaas (2009).
Low pH-triggered beta-propeller switch of the low-density lipoprotein receptor assists rhinovirus infection.
  J Virol, 83, 10922-10930.  
19582713 V.U.Weiss, G.Bilek, A.Pickl-Herk, D.Blaas, and E.Kenndler (2009).
Mimicking virus attachment to host cells employing liposomes: analysis by chip electrophoresis.
  Electrophoresis, 30, 2123-2128.  
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.