7fab

From Proteopedia

(Difference between revisions)

Current revision

CRYSTAL STRUCTURE OF HUMAN IMMUNOGLOBULIN FRAGMENT FAB NEW REFINED AT 2.0 ANGSTROMS RESOLUTION

Structural highlights

7fab is a 2 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entries 3fab, 2fab and 1fab. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IGLC2_HUMAN Constant region of immunoglobulin light chains. Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268).^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The three-dimensional structure of the human immunoglobulin fragment Fab New (IgG1, lambda) has been refined to a crystallographic R-factor of 16.9% to 2 A resolution. Rms deviations of the final model from ideal geometry are 0.014 A for bond distances and 3.03 degrees for bond angles. Refinement was based on a new X-ray data set including 28,301 reflections with F > 2.5 sigma(F) from 6.0 to 2.0 A resolution. The starting model for the refinement procedure reported here is from the Brookhaven Protein Data Bank entry 3FAB (rev. 1981). Differences between the initial and final models include modified polypeptide-chain folding in the third complementarity-determining region (CDR3) and the third framework region (FR3) of VH and in some exposed loops of CL and CH1. Amino acid sequence changes were determined at a number of positions by inspection of difference electron density maps. The incorporation of amino acid sequence changes results in an improved VH framework model for the "humanization" of monoclonal antibodies.

Crystal structure of human immunoglobulin fragment Fab New refined at 2.0 A resolution.,Saul FA, Poljak RJ Proteins. 1992 Nov;14(3):363-71. PMID:1438175^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Teng G, Papavasiliou FN. Immunoglobulin somatic hypermutation. Annu Rev Genet. 2007;41:107-20. PMID:17576170 doi:http://dx.doi.org/10.1146/annurev.genet.41.110306.130340
↑ Schroeder HW Jr, Cavacini L. Structure and function of immunoglobulins. J Allergy Clin Immunol. 2010 Feb;125(2 Suppl 2):S41-52. doi:, 10.1016/j.jaci.2009.09.046. PMID:20176268 doi:http://dx.doi.org/10.1016/j.jaci.2009.09.046
↑ McHeyzer-Williams M, Okitsu S, Wang N, McHeyzer-Williams L. Molecular programming of B cell memory. Nat Rev Immunol. 2011 Dec 9;12(1):24-34. doi: 10.1038/nri3128. PMID:22158414 doi:http://dx.doi.org/10.1038/nri3128
↑ Saul FA, Poljak RJ. Crystal structure of human immunoglobulin fragment Fab New refined at 2.0 A resolution. Proteins. 1992 Nov;14(3):363-71. PMID:1438175 doi:http://dx.doi.org/10.1002/prot.340140305

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7fab"

Categories: Homo sapiens | Large Structures | Poljak RJ | Saul F

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF HUMAN IMMUNOGLOBULIN FRAGMENT FAB NEW REFINED AT 2.0 ANGSTROMS RESOLUTION==
-<StructureSection load='7fab' size='340' side='right' caption='[[7fab]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='7fab' size='340' side='right'caption='[[7fab]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7fab]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fab 3fab], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fab 2fab] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fab 1fab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7FAB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7fab]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fab 3fab], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fab 2fab] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fab 1fab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FAB FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7fab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fab OCA], [http://pdbe.org/7fab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7fab RCSB], [http://www.ebi.ac.uk/pdbsum/7fab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7fab ProSAT]</span></td></tr>
+</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&#8491;</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=7fab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fab OCA], [https://pdbe.org/7fab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fab RCSB], [https://www.ebi.ac.uk/pdbsum/7fab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fab ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/IGLC2_HUMAN IGLC2_HUMAN] Constant region of immunoglobulin light chains. Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268).<ref>PMID:17576170</ref> <ref>PMID:20176268</ref> <ref>PMID:22158414</ref>
 == 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/fa/7fab_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/7fab_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 27: / Line 30: @@
 ==See Also==
-*[[3D structures of antibody|3D structures of antibody]]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Sandbox 20009|Sandbox 20009]]
+*[[3D structures of human antibody|3D structures of human antibody]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Poljak, R J]]
+[[Category: Large Structures]]
-[[Category: Saul, F]]
+[[Category: Poljak RJ]]
-[[Category: Immune system]]
+[[Category: Saul F]]
-[[Category: Immunoglobulin]]

7fab

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF HUMAN IMMUNOGLOBULIN FRAGMENT FAB NEW REFINED AT 2.0 ANGSTROMS RESOLUTION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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