PDBsum entry 1i9j

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Immune system PDB id
Protein chains
219 a.a. *
220 a.a. *
Waters ×337
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Testosterone complex structure of the recombinant monoclonal wild type anti-testosterone fab fragment
Structure: Recombinant monoclonal anti-testosterone fab fragment light chain. Chain: l. Engineered: yes. Recombinant monoclonal anti-testosterone fab fragment heavy chain. Chain: h. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.60Å     R-factor:   0.188     R-free:   0.255
Authors: J.Valjakka,K.Takkinenz,T.Teerinen,H.Soderlund,J.Rouvinen
Key ref:
J.Valjakka et al. (2002). Structural insights into steroid hormone binding: the crystal structure of a recombinant anti-testosterone Fab fragment in free and testosterone-bound forms. J Biol Chem, 277, 4183-4190. PubMed id: 11707437 DOI: 10.1074/jbc.M105579200
20-Mar-01     Release date:   20-Mar-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q65ZC0  (Q65ZC0_MOUSE) -  Kappa light chain C_region (Fragment)
219 a.a.
219 a.a.*
Protein chain
Pfam   ArchSchema ?
Q91Z05  (Q91Z05_MOUSE) -  Ighg protein
473 a.a.
220 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 69 residue positions (black crosses)


DOI no: 10.1074/jbc.M105579200 J Biol Chem 277:4183-4190 (2002)
PubMed id: 11707437  
Structural insights into steroid hormone binding: the crystal structure of a recombinant anti-testosterone Fab fragment in free and testosterone-bound forms.
J.Valjakka, K.Takkinenz, T.Teerinen, H.Söderlund, J.Rouvinen.
The monoclonal anti-testosterone antibody (3-C(4)F(5)) has a relatively high affinity (3 x 10(8) m(-1)) with an overall good specificity profile. However, the earlier characterized binding properties have shown that both the affinity and specificity of this antibody must be improved if it is intended for use in clinical immunoassays. In this paper, the crystal structures of the recombinant anti-testosterone (3-C(4)F(5)) Fab fragment have been determined in the testosterone-bound and free form at resolutions of 2.60 and 2.72 A, respectively. The high affinity binding of the (3-C(4)F(5)) Fab is mainly determined by shape complementarity between the protein and testosterone. Only one direct hydrogen bond is formed between the hydroxyl group of the testosterone D-ring and the main-chain oxygen of Gly100(J)H. The testosterone is deeply bound in a hydrophobic pocket, and the close shape complementarity is mainly formed by the third complementarity-determining regions (CDR) of the heavy and light chain. Comparison of the bound structure with the free structure indicates conformational changes in the protein upon testosterone binding. The conformational changes of the side chains of two residues Glu95H and Tyr99H in the CDR-H3 are particularly essential for the binding. Interesting similarities in the binding of different steroids were also observed upon comparison of the available structures of anti-steroid antibodies.
  Selected figure(s)  
Figure 8.
Fig. 8. Comparison of the binding mechanism of the anti-testosterone Fab (top), anti-progesterone Fab DB3 (5) (middle), and anti-digoxin Fab (8) (bottom). The free structures are shown in pink and steroid complexes in black. Stereopairs were prepared with the Molscript program (41).
Figure 10.
Fig. 10. Schematic diagrams of the steroid binding sites. A, the anti-testosterone Fab; B, the anti-progesterone Fab (5); C, the anti-digoxin Fab 26-10 (8), and D, the Fv4155 (10) fragments.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 4183-4190) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21360611 M.H.Niemi, K.Takkinen, L.K.Amundsen, H.Söderlund, J.Rouvinen, and M.Höyhtyä (2011).
The testosterone binding mechanism of an antibody derived from a naïve human scFv library.
  J Mol Recognit, 24, 209-219.
PDB code: 3kdm
17252586 M.J.Bobeck, and G.D.Glick (2007).
Role of conformational dynamics in sequence-specific autoantibody*ssDNA recognition.
  Biopolymers, 85, 481-489.  
14997538 T.Laitinen, J.A.Kankare, and M.Peräkylä (2004).
Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody.
  Proteins, 55, 34-43.  
12471606 N.Nordman, J.Valjakka, and M.Peräkylä (2003).
Analysis of the binding energies of testosterone, 5alpha-dihydrotestosterone, androstenedione and dehydroepiandrosterone sulfate with an antitestosterone antibody.
  Proteins, 50, 135-143.  
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.