PDBsum entry 2o5x

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Immune system PDB id
Protein chains
218 a.a. *
219 a.a. *
SO4 ×11
Waters ×278
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Crystal structure of 1e9 leuh47trp/argh100trp, an engineered alderase fab with nm steroid-binding affinity
Structure: Chimeric antibody fab 1e9-db3. Chain: l. Fragment: light chain. Engineered: yes. Mutation: yes. Chimeric antibody fab 1e9-db3. Chain: h. Fragment: heavy chain. Engineered: yes.
Source: Mus musculus, homo sapiens. House mouse, human. Organism_taxid: 10090,9606. Strain: ,. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.05Å     R-factor:   0.179     R-free:   0.204
Authors: P.Verdino,I.A.Wilson
Key ref:
P.Verdino et al. (2008). Closely related antibody receptors exploit fundamentally different strategies for steroid recognition. Proc Natl Acad Sci U S A, 105, 11725-11730. PubMed id: 18689687 DOI: 10.1073/pnas.0801783105
06-Dec-06     Release date:   18-Dec-07    
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Protein chain
No UniProt id for this chain
Struc: 218 a.a.
Protein chain
No UniProt id for this chain
Struc: 219 a.a.
Key:    Secondary structure  CATH domain


DOI no: 10.1073/pnas.0801783105 Proc Natl Acad Sci U S A 105:11725-11730 (2008)
PubMed id: 18689687  
Closely related antibody receptors exploit fundamentally different strategies for steroid recognition.
P.Verdino, C.Aldag, D.Hilvert, I.A.Wilson.
Molecular recognition by the adaptive immune system relies on specific high-affinity antibody receptors that are generated from a restricted set of starting sequences through homologous recombination and somatic mutation. The steroid binding antibody DB3 and the catalytic Diels-Alderase antibody 1E9 derive from the same germ line sequences but exhibit very distinct specificities and functions. However, mutation of only two of the 36 sequence differences in the variable domains, Leu(H47)Trp and Arg(H100)Trp, converts 1E9 into a high-affinity steroid receptor with a ligand recognition profile similar to DB3. To understand how these changes switch binding specificity and function, we determined the crystal structures of the 1E9 Leu(H47)Trp/Arg(H100)Trp double mutant (1E9dm) as an unliganded Fab at 2.05 A resolution and in complex with two configurationally distinct steroids at 2.40 and 2.85 A. Surprisingly, despite the functional mimicry of DB3, 1E9dm employs a distinct steroid binding mechanism. Extensive structural rearrangements occur in the combining site, where residue H47 acts as a specificity switch and H100 adapts to different ligands. Unlike DB3, 1E9dm does not use alternative binding pockets or different sets of hydrogen-bonding interactions to bind configurationally distinct steroids. Rather, the different steroids are inserted more deeply into the 1E9dm combining site, creating more hydrophobic contacts that energetically compensate for the lack of hydrogen bonds. These findings demonstrate how subtle mutations within an existing molecular scaffold can dramatically modulate the function of immune receptors by inducing unanticipated, but compensating, mechanisms of ligand interaction.
  Selected figure(s)  
Figure 3.
Ligand binding by Diels–Alderase 1E9 (A), 1E9dm (B), and the steroid-binding DB3 (C). (Left) Proteins are shown in the same orientation to demonstrate the distinct shapes of the combining sites and the different ways in which the respective ligands are bound. Light yellow, 1E9 TSA; cyan, progesterone; orange, 5β-androstane-3,17-dione and two ordered water molecules. (Right) 2D schemes of the ligand binding modes are shown. Green, polar residues; brown, hydrophobic; blue-lined circle, basic; red-lined circle, acidic; gray dashed line, proximity contour; fuzzy blue, ligand exposure; blue underlayed circle, receptor exposure; green arrow, side chain donor; olive line, solvent contact.
Figure 4.
Overlay of the combining sites of 1E9, 1E9dm, and DB3 with bound ligands. (A) 1E9 and its TSA (gray) superimposed with 1E9dm binding progesterone (cyan). This view is rotated around the z axis ≈90° compared with B–D to demonstrate the movement of the Trp^H50 side chain in 1E9dm caused by the Leu^H47Trp mutation. (B) The TSA bound by 1E9 (gray) and 5β-androstane-3,17-dione bound by 1E9dm (orange). (C) Progesterone bound by 1E9dm in the inverse head-to-tail binding mode with a buried A ring (cyan). The same steroid bound by DB3 (gray). (D) 5β-androstane-3,17-dione bound by 1E9dm (orange) and DB3 (gray).
  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
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