1igt: Difference between revisions

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-[[Image:1igt.png|left|200px]]
-{{STRUCTURE_1igt|  PDB=1igt  |  SCENE=  }}
+==STRUCTURE OF IMMUNOGLOBULIN==
+<StructureSection load='1igt' size='340' side='right'caption='[[1igt]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1igt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. The September 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Antibodies''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_9 10.2210/rcsb_pdb/mom_2001_9]. The February 2005 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Major Histocompatibility Complex''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2005_2 10.2210/rcsb_pdb/mom_2005_2]. The May 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ricin''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_5 10.2210/rcsb_pdb/mom_2013_5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IGT FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1igt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1igt OCA], [https://pdbe.org/1igt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1igt RCSB], [https://www.ebi.ac.uk/pdbsum/1igt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1igt ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GCAA_MOUSE GCAA_MOUSE]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/1igt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1igt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of an intact, anti-canine lymphoma monoclonal antibody (Mab231) was determined by molecular replacement and refined in a triclinic cell to an R-value of 20.9%, using synchrotron diffraction data from 2.8 to 20 A resolution. All segments of the antibody, including the hinge region and carbohydrate component, are visible in electron density maps. There is no overall symmetry to the antibody, as the Fc is disposed in an entirely oblique manner with respect to the Fabs. The CH2 and CH3 domains do, however, possess a nearly exact, local 2-fold relationship. The Fab segments are related by a second, independent, local dyad axis, exact only with respect to constant domains. Variable domains exhibit no symmetry relationship as a consequence of the 16 degrees difference in Fab elbow angles. Variable domain pair associations VL:VH for the Fabs are virtually the same, and corresponding CDRs of the two Fabs also are nearly identical in structure. CDR-H3 displays the greatest difference. Hypervariable loops of both Fabs are involved in contacts with symmetry-related Fc segments at the CH2-CH3 switch junction, suggesting a "complex" structure. The hinge segment connecting Fabs with the Fc is quite extended and exhibits thermal factors indicative of a high degree of mobility. It consists of a well-defined upper hinge that partially maintains dyad symmetry and a fairly rigid core bounded above and below by fluid polypeptides that provide segmental flexibility. This structure represents the first visualization by X-ray analysis of a murine Fc segment, and its CH2 domains exhibit substantial rigid body conformational changes with respect to the human Fc used as an initial molecular replacement model. The oligosaccharides were found by difference Fourier syntheses to be very similar to those of the free human Fc fragment, although differences are present in the terminal residues. The detailed structure of the IgG presented here, and the distribution of effector binding sites, appears consistent with effector activation mechanisms involving translocation and/or aggregation of the Fc following antigen binding by the Fabs.
-===STRUCTURE OF IMMUNOGLOBULIN===
+Refined structure of an intact IgG2a monoclonal antibody.,Harris LJ, Larson SB, Hasel KW, McPherson A Biochemistry. 1997 Feb 18;36(7):1581-97. PMID:9048542<ref>PMID:9048542</ref>
-{{ABSTRACT_PUBMED_9048542}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1igt" style="background-color:#fffaf0;"></div>
-[[1igt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. The September 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Antibodies''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_9 10.2210/rcsb_pdb/mom_2001_9]. The February 2005 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Major Histocompatibility Complex''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2005_2 10.2210/rcsb_pdb/mom_2005_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IGT OCA].
 ==See Also==
 *[[Antibody|Antibody]]
-*[[Homology modeling servers|Homology modeling servers]]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-*[[Monoclonal Antibody|Monoclonal Antibody]]
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:009048542</ref><ref group="xtra">PMID:011021535</ref><ref group="xtra">PMID:016287250</ref><references group="xtra"/>
+</StructureSection>
 [[Category: Antibodies]]
+[[Category: Large Structures]]
 [[Category: Major Histocompatibility Complex]]
 [[Category: Mus musculus]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Harris, L J.]]
+[[Category: Ricin]]
-[[Category: Hasel, K W.]]
+[[Category: Harris LJ]]
-[[Category: Larson, S B.]]
+[[Category: Hasel KW]]
-[[Category: McPherson, A.]]
+[[Category: Larson SB]]
-[[Category: Immunoglobulin]]
+[[Category: McPherson A]]
-[[Category: Intact immunoglobulin v region c region]]