1p7k

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[[Image:1p7k.gif|left|200px]]
[[Image:1p7k.gif|left|200px]]
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{{Structure
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|PDB= 1p7k |SIZE=350|CAPTION= <scene name='initialview01'>1p7k</scene>, resolution 1.75&Aring;
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The line below this paragraph, containing "STRUCTURE_1p7k", creates the "Structure Box" on the page.
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|SITE=
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|LIGAND= <scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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|GENE=
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{{STRUCTURE_1p7k| PDB=1p7k | SCENE= }}
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|RELATEDENTRY=[[1i8m|1I8M]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7k OCA], [http://www.ebi.ac.uk/pdbsum/1p7k PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1p7k RCSB]</span>
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'''Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES)'''
'''Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES)'''
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[[Category: Schuermann, J P.]]
[[Category: Schuermann, J P.]]
[[Category: Tanner, J J.]]
[[Category: Tanner, J J.]]
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[[Category: anti-dna antibody]]
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[[Category: Anti-dna antibody]]
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[[Category: antibody]]
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[[Category: Antibody]]
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[[Category: autoantibody]]
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[[Category: Autoantibody]]
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[[Category: fab]]
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[[Category: Fab]]
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[[Category: hepe]]
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[[Category: Hepe]]
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[[Category: lupus]]
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[[Category: Lupus]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:47:01 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:55:58 2008''
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Revision as of 01:47, 3 May 2008

Image:1p7k.gif

Template:STRUCTURE 1p7k

Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES)


Overview

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.

About this Structure

1P7K is a Protein complex structure of sequences from Mus musculus. Full crystallographic information is available from OCA.

Reference

Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry., Schuermann JP, Henzl MT, Deutscher SL, Tanner JJ, Proteins. 2004 Nov 1;57(2):269-78. PMID:15340914 Page seeded by OCA on Sat May 3 04:47:01 2008

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