PDBsum entry 1p7k

Immune system

PDB id: 1p7k

Contents

Protein chains

213 a.a. *

220 a.a. *

Ligands

SO4 ×9

EPE ×2

1PE ×4

PEG ×2

GOL ×16

Waters ×771

* Residue conservation analysis

PDB id:

1p7k

Name:

Immune system

Title:

Crystal structure of an anti-ssdna antigen-binding fragment (fab) bound to 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid (hepes)

Structure:

Antibody light chain fab. Chain: l, a. Engineered: yes. Antibody heavy chain fab. Chain: h, b. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.75Å R-factor: 0.197 R-free: 0.230

Authors:

J.P.Schuermann,M.T.Henzl,S.L.Deutscher,J.J.Tanner

Key ref:

J.P.Schuermann et al. (2004). Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry. Proteins, 57, 269-278. PubMed id: 15340914 DOI: 10.1002/prot.20200

Date:

02-May-03 Release date: 11-May-04

Protein chains

I6L978  (I6L978_MOUSE) -  Igk protein from Mus musculus

Seq: 234 a.a.

Struc: 213 a.a.*

Protein chains

P01868  (IGHG1_MOUSE) -  Ig gamma-1 chain C region secreted form from Mus musculus

Seq: 324 a.a.

Struc: 220 a.a.*

* PDB and UniProt seqs differ at 12 residue positions (black crosses)

DOI no: 10.1002/prot.20200

Proteins 57:269-278 (2004)

PubMed id: 15340914

Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry.

J.P.Schuermann, M.T.Henzl, S.L.Deutscher, J.J.Tanner.

ABSTRACT

Antibodies that recognize DNA (anti-DNA) are part of the autoimmune response underlying systemic lupus erythematosus. To better understand molecular recognition by anti-DNA antibodies, crystallographic studies have been performed using an anti-ssDNA antigen-binding fragment (Fab) known as DNA-1. The previously determined structure of a DNA-1/dT5 complex revealed that thymine bases insert into a narrow groove, and that ligand recognition primarily involves the bases of DNA. We now report the 1.75-A resolution structure of DNA-1 complexed with the biological buffer HEPES (4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid). All three light chain complementarity-determining regions (CDRs) and HCDR3 contribute to binding. The HEPES sulfonate hydrogen bonds to His L91, Asn L50, and to the backbone of Tyr H100 and Tyr H100A. The Tyr side-chains of L32, L92, H100, and H100A form nonpolar contacts with the HEPES ethylene and piperazine groups. Comparison to the DNA-1/dT5 structure reveals that the dual recognition of dT5 and HEPES requires a 13-A movement of HCDR3. This dramatic structural change converts the combining site from a narrow groove, appropriate for the edge-on insertion of thymine bases, to one sufficiently wide to accommodate the HEPES sulfonate and piperazine. Isothermal titration calorimetry verified the association of HEPES with DNA-1 under conditions similar those used for crystallization (2 M ammonium sulfate). Interestingly, the presence of 2 M ammonium sulfate increases the affinities of DNA-1 for both HEPES and dT5, suggesting that non-polar Fab-ligand interactions are important for molecular recognition in highly ionic solvent conditions. The structural and thermodynamic data suggest a molecular mimicry mechanism based on structural plasticity and hydrophobic interactions.

Selected figure(s)

Figure 3.
Figure 3. Stereo-view of the DNA-1/HEPES binding site highlighting Fab-ligand interactions. The HEPES and sulfate ligands appear in yellow and green; protein side-chains are colored white. The dotted lines denote hydrogen bonds and ion pairs. The orientation of the protein depicted in this figure is identical to those of Figures 1 and 4.

Figure 4.
Figure 4. Stereo-view of Fab-DNA interactions from DNA-1/dT[5] structure (PDB code 1I8M).[16] DNA appears in yellow, while protein side-chains are colored white. The dotted lines denote hydrogen bonds. The orientation of the protein depicted in this figure is identical to those of Figures 1 and 3.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 57, 269-278) copyright 2004.

Figures were selected by the author.