1dql

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[[Image:1dql.jpg|left|200px]]
 
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==CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY==
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The line below this paragraph, containing "STRUCTURE_1dql", creates the "Structure Box" on the page.
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<StructureSection load='1dql' size='340' side='right'caption='[[1dql]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1dql]] is a 2 chain structure with sequence from [https://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]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQL FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
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{{STRUCTURE_1dql| PDB=1dql | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dql OCA], [https://pdbe.org/1dql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dql RCSB], [https://www.ebi.ac.uk/pdbsum/1dql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dql ProSAT]</span></td></tr>
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</table>
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'''CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY'''
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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==Overview==
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<jmolCheckbox>
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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.
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/1dql_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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==About this Structure==
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<text>to colour the structure by Evolutionary Conservation</text>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQL OCA].
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dql ConSurf].
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==Reference==
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<div style="clear:both"></div>
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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]
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__TOC__
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[[Category: Edmundson, A B.]]
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</StructureSection>
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[[Category: Guddat, L W.]]
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[[Category: Homo sapiens]]
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[[Category: Moomaw, C R.]]
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[[Category: Large Structures]]
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[[Category: Ramsland, P A.]]
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[[Category: Edmundson AB]]
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[[Category: Shan, L.]]
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[[Category: Guddat LW]]
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[[Category: Slaughter, C A.]]
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[[Category: Moomaw CR]]
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[[Category: Antibody]]
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[[Category: Ramsland PA]]
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[[Category: Fv]]
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[[Category: Shan L]]
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[[Category: Igm]]
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[[Category: Slaughter CA]]
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[[Category: Immunoglobulin fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 14:09:30 2008''
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Current revision

CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY

PDB ID 1dql

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