1dql
From Proteopedia
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| - | [[Image:1dql.jpg|left|200px]] | + | [[Image:1dql.jpg|left|200px]] |
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| - | '''CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY''' | + | {{Structure |
| + | |PDB= 1dql |SIZE=350|CAPTION= <scene name='initialview01'>1dql</scene>, resolution 2.6Å | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
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| + | '''CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1DQL is a [ | + | 1DQL is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQL OCA]. |
==Reference== | ==Reference== | ||
| - | An unusual human IgM antibody with a protruding HCDR3 and high avidity for its peptide ligands., Ramsland PA, Shan L, Moomaw CR, Slaughter CA, Fan Z, Guddat LW, Edmundson AB, Mol Immunol. 2000 Apr;37(6):295-310. PMID:[http:// | + | An unusual human IgM antibody with a protruding HCDR3 and high avidity for its peptide ligands., Ramsland PA, Shan L, Moomaw CR, Slaughter CA, Fan Z, Guddat LW, Edmundson AB, Mol Immunol. 2000 Apr;37(6):295-310. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11000403 11000403] |
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
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[[Category: immunoglobulin fold]] | [[Category: immunoglobulin fold]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:42:43 2008'' |
Revision as of 08:42, 20 March 2008
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| , resolution 2.6Å | |||||||
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY
Overview
The crystal structure of the Fv molecule from a human monoclonal IgM cryoglobulin (Mez) was determined at 2.6 A resolution. Amino acid sequences of framework regions (FR) of the Mez light (L) and heavy (H) chain variable domains (VL and VH) are highly similar to their counterparts in another human Fv (Pot) previously subjected to X-ray analysis in our laboratory. As expected, the three-dimensional (3-D) structures of FR are quite similar in the two proteins, as are four of the six complementarity-determining regions (CDRs): CDRs 1 and 2 for both L and H chains. Absence of Pro 95L from the LCDR3 loop in Mez VL (relative to Pot LCDR3) results in compression of this loop and creates more space in the VL-VH interface. In the two IgMs, HCDR3 conformations differ significantly from all previously defined conformations for these loops. Pot has a 12-residue HCDR3 that collapses to fill all available space in the VL-VH domain interface, resulting in the formation of a relatively flat platform for antigen binding. In Mez, the HCDR3 is two residues longer and is comprehensively different. A semi-rigid ascending segment dominated by a Pro-Pro-Tyr sequence protrudes out into solvent. The descending portion has the sequence Gly-Trp-Gly-Gly-Gly, which promotes high local flexibility. This segment folds across the VL-VH domain interface to interact with residues in LCDR3. These features partition the Mez active site into two compartments, a large cavity between VL and VH and a smaller cavity lined entirely by constituents of the three heavy chain CDRs. Such an unusual topographical feature indicates why the Mez IgM does not bind to the Fc portion of intact human IgG antibodies in immunoassays yet interacts with high avidity with many Fc-derived octapeptides. The cavities are expected to be the repositories for the Fc-derived peptides, while the semi-rigid protrusion of the Mez HCDR3 prevents the close approach of another macromolecule (e.g. intact IgG) to the active site.
About this Structure
1DQL is a Protein complex structure of sequences from Homo sapiens. Full crystallographic information is available from OCA.
Reference
An unusual human IgM antibody with a protruding HCDR3 and high avidity for its peptide ligands., Ramsland PA, Shan L, Moomaw CR, Slaughter CA, Fan Z, Guddat LW, Edmundson AB, Mol Immunol. 2000 Apr;37(6):295-310. PMID:11000403
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