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PDBsum entry 3d87

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protein ligands metals Protein-protein interface(s) links
Cytokine PDB id
3d87
Jmol
Contents
Protein chains
161 a.a. *
298 a.a. *
159 a.a. *
Ligands
MAN
PO4 ×2
Metals
__K ×2
* Residue conservation analysis
PDB id:
3d87
Name: Cytokine
Title: Crystal structure of interleukin-23
Structure: Interleukin-23 subunit p19. Chain: a, c. Fragment: subunit p19. Synonym: interleukin-23 subunit alpha. Il-23 subunit alpha. Il-23p19. Engineered: yes. Interleukin-12 subunit p40. Chain: b, d. Fragment: subunit p40.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: il23a, sgrf, unq2498/pro5798. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: hi-five cells. Gene: il12b, nksf2.
Resolution:
2.90Å     R-factor:   0.269     R-free:   0.323
Authors: B.M.Beyer,R.Ingram,L.Ramanathan,P.Reichert,H.Le,V.Madison
Key ref:
B.M.Beyer et al. (2008). Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody. J Mol Biol, 382, 942-955. PubMed id: 18708069 DOI: 10.1016/j.jmb.2008.08.001
Date:
22-May-08     Release date:   02-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9NPF7  (IL23A_HUMAN) -  Interleukin-23 subunit alpha
Seq:
Struc:
189 a.a.
161 a.a.
Protein chains
Pfam   ArchSchema ?
P29460  (IL12B_HUMAN) -  Interleukin-12 subunit beta
Seq:
Struc:
328 a.a.
298 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9NPF7  (IL23A_HUMAN) -  Interleukin-23 subunit alpha
Seq:
Struc:
189 a.a.
159 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   6 terms 
  Biological process     immune system process   64 terms 
  Biochemical function     protein binding     11 terms  

 

 
DOI no: 10.1016/j.jmb.2008.08.001 J Mol Biol 382:942-955 (2008)
PubMed id: 18708069  
 
 
Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody.
B.M.Beyer, R.Ingram, L.Ramanathan, P.Reichert, H.V.Le, V.Madison, P.Orth.
 
  ABSTRACT  
 
Interleukin (IL)-23 is a pro-inflammatory cytokine playing a key role in the pathogenesis of several autoimmune and inflammatory diseases. We have determined the crystal structures of the heterodimeric p19-p40 IL-23 and its complex with the Fab (antigen-binding fragment) of a neutralizing antibody at 2.9 and 1.9 A, respectively. The IL-23 structure closely resembles that of IL-12. They share the common p40 subunit, and IL-23 p19 overlaps well with IL-12 p35. Along the hydrophilic heterodimeric interface, fewer charged residues are involved for IL-23 compared with IL-12. The binding site of the Fab is located exclusively on the p19 subunit, and comparison with published cytokine-receptor structures suggests that it overlaps with the IL-23 receptor binding site.
 
  Selected figure(s)  
 
Figure 6.
Fig. 6. Unfolded C-terminus of p19 helix B is recognized by 7G10. Hydrogen bonds are shown as dotted lines. Tyr54 forms hydrophobic interactions with Gly86.
Figure 10.
Fig. 10. Specific interactions along the p19–7G10 interface. (a) His92^L and p19 residue Trp137 form an aromatic stacking. A larger aromatic residue, such as Trp or Tyr, would improve these interactions. (b) Tyr54^H hydrogen bonds to Glu82 and His106 and forms hydrophobic contact with Gly86. (c) p19 residues Glu93 and Arg139 are buried within the 7G10–p19 interface. The side chain of Phe94^L is 3.8 Å apart from Arg139. Mutating Phe94^L residue into a Tyr would create an additional hydrogen bond. Additionally, modifying Lys59^H into a medium-sized hydrophobic group, such as Ile or Leu, might improve the van der Waals contacts with Phe94^L and Pro133 of p19. (d) Side-chain interactions between Tyr32^L and Tyr50^L and Pro50 as well as Asp101^H and Ser95.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 382, 942-955) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
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