1edl: Difference between revisions
New page: left|200px<br /><applet load="1edl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1edl" /> '''STAPHYLOCOCCAL PROTEIN A E-DOMAIN (-60), NMR... |
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== | ==STAPHYLOCOCCAL PROTEIN A E-DOMAIN (-60), NMR, 22 STRUCTURES== | ||
The E-domain of staphylococcal protein A is one of five homologous | <StructureSection load='1edl' size='340' side='right'caption='[[1edl]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1edl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EDL FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1edl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1edl OCA], [https://pdbe.org/1edl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1edl RCSB], [https://www.ebi.ac.uk/pdbsum/1edl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1edl ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/SPA_STAAU SPA_STAAU] | |||
== 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/ed/1edl_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1edl ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The E-domain of staphylococcal protein A is one of five homologous IgG-binding domains designated E, D, A, B, and C that comprise the extracellular portion of protein A. The E-domain binds tightly to Fc fragments of IgG and binds certain Fv fragments with micromolar affinity. To explore further the structural features of Fc binding by protein A, and as a first step in developing a structural understanding of E-domain/Fv complex formation, we have determined the solution structure of the uncomplexed E-domain using 2D homonuclear and heteronuclear NMR spectroscopy. Complete 1H and 15N resonance assignments were obtained, and the structure was determined from 383 NOE-derived distance restrains, 34 phi and 19 chi 1 dihedral angle restraints, and 54 restraints for 27 H-bonds. 3JH alpha-H beta coupling constants and long-range NOEs involving Phe11 indicate the side chain exists in more than one conformation with differing chi 1 values. NOE restraints that were incompatible with chi 1 = -60 degrees were removed from one set of structure calculations, and those incompatible with chi 1 = 180 degrees were removed from a second set to allow Phe11 to explore both rotamer wells. Thus, two sets of 20 final structures, having no distance or dihedral angle restraint violations greater than 0.12 A or 1.6 degrees, respectively, represent the solution structure of the E-domain. Backbone atomic rms differences with respect to the mean coordinates for each set of 20 structures for residues 8-53 averaged 0.41 +/- 0.06 and 0.35 +/- 0.06 A. No significant differences in the overall structure result from the different orientations of Phe11. The solution structure of the E-domain consists of three alpha-helices that pack together to form a compact helical bundle. A detailed comparison between the E-domain ensembles and the previously determined structure for the B-domain in complex with Fc indicates that only the 180 degrees chi 1 rotamer of Phe11 is competent for binding; the -60 degrees chi 1 rotamer must reorient to 180 degrees to create a cavity that is filled by Ile253 from the CH2 domain of Fc in the Fc-bound complex. | |||
Solution structure of the E-domain of staphylococcal protein A.,Starovasnik MA, Skelton NJ, O'Connell MP, Kelley RF, Reilly D, Fairbrother WJ Biochemistry. 1996 Dec 3;35(48):15558-69. PMID:8952510<ref>PMID:8952510</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 1edl" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Staphylococcus aureus]] | [[Category: Staphylococcus aureus]] | ||
[[Category: Fairbrother | [[Category: Fairbrother WJ]] | ||
[[Category: Skelton | [[Category: Skelton NJ]] | ||
[[Category: Starovasnik | [[Category: Starovasnik MA]] | ||
Latest revision as of 11:25, 22 May 2024
STAPHYLOCOCCAL PROTEIN A E-DOMAIN (-60), NMR, 22 STRUCTURESSTAPHYLOCOCCAL PROTEIN A E-DOMAIN (-60), NMR, 22 STRUCTURES
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe E-domain of staphylococcal protein A is one of five homologous IgG-binding domains designated E, D, A, B, and C that comprise the extracellular portion of protein A. The E-domain binds tightly to Fc fragments of IgG and binds certain Fv fragments with micromolar affinity. To explore further the structural features of Fc binding by protein A, and as a first step in developing a structural understanding of E-domain/Fv complex formation, we have determined the solution structure of the uncomplexed E-domain using 2D homonuclear and heteronuclear NMR spectroscopy. Complete 1H and 15N resonance assignments were obtained, and the structure was determined from 383 NOE-derived distance restrains, 34 phi and 19 chi 1 dihedral angle restraints, and 54 restraints for 27 H-bonds. 3JH alpha-H beta coupling constants and long-range NOEs involving Phe11 indicate the side chain exists in more than one conformation with differing chi 1 values. NOE restraints that were incompatible with chi 1 = -60 degrees were removed from one set of structure calculations, and those incompatible with chi 1 = 180 degrees were removed from a second set to allow Phe11 to explore both rotamer wells. Thus, two sets of 20 final structures, having no distance or dihedral angle restraint violations greater than 0.12 A or 1.6 degrees, respectively, represent the solution structure of the E-domain. Backbone atomic rms differences with respect to the mean coordinates for each set of 20 structures for residues 8-53 averaged 0.41 +/- 0.06 and 0.35 +/- 0.06 A. No significant differences in the overall structure result from the different orientations of Phe11. The solution structure of the E-domain consists of three alpha-helices that pack together to form a compact helical bundle. A detailed comparison between the E-domain ensembles and the previously determined structure for the B-domain in complex with Fc indicates that only the 180 degrees chi 1 rotamer of Phe11 is competent for binding; the -60 degrees chi 1 rotamer must reorient to 180 degrees to create a cavity that is filled by Ile253 from the CH2 domain of Fc in the Fc-bound complex. Solution structure of the E-domain of staphylococcal protein A.,Starovasnik MA, Skelton NJ, O'Connell MP, Kelley RF, Reilly D, Fairbrother WJ Biochemistry. 1996 Dec 3;35(48):15558-69. PMID:8952510[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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