2kpf: Difference between revisions

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 ==Spatial structure of the dimeric transmembrane domain of glycophorin A in bicelles soluton==
-<StructureSection load='2kpf' size='340' side='right' caption='[[2kpf]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2kpf' size='340' side='right'caption='[[2kpf]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2kpf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KPF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KPF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2kpf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KPF FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2kpe|2kpe]]</td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GYPA, GPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2kpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kpf OCA], [https://pdbe.org/2kpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kpf RCSB], [https://www.ebi.ac.uk/pdbsum/2kpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kpf ProSAT]</span></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=2kpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kpf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kpf RCSB], [http://www.ebi.ac.uk/pdbsum/2kpf PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GLPA_HUMAN GLPA_HUMAN]] Glycophorin A is the major intrinsic membrane protein of the erythrocyte. The N-terminal glycosylated segment, which lies outside the erythrocyte membrane, has MN blood group receptors. Appears to be important for the function of SLC4A1 and is required for high activity of SLC4A1. May be involved in translocation of SLC4A1 to the plasma membrane. Is a receptor for influenza virus. Is a receptor for Plasmodium falciparum erythrocyte-binding antigen 175 (EBA-175); binding of EBA-175 is dependent on sialic acid residues of the O-linked glycans. Appears to be a receptor for Hepatitis A virus (HAV).<ref>PMID:8009226</ref> <ref>PMID:10926825</ref> <ref>PMID:12813056</ref> <ref>PMID:14604989</ref> <ref>PMID:15331714</ref> <ref>PMID:19438409</ref>
+[https://www.uniprot.org/uniprot/GLPA_HUMAN GLPA_HUMAN] Glycophorin A is the major intrinsic membrane protein of the erythrocyte. The N-terminal glycosylated segment, which lies outside the erythrocyte membrane, has MN blood group receptors. Appears to be important for the function of SLC4A1 and is required for high activity of SLC4A1. May be involved in translocation of SLC4A1 to the plasma membrane. Is a receptor for influenza virus. Is a receptor for Plasmodium falciparum erythrocyte-binding antigen 175 (EBA-175); binding of EBA-175 is dependent on sialic acid residues of the O-linked glycans. Appears to be a receptor for Hepatitis A virus (HAV).<ref>PMID:8009226</ref> <ref>PMID:10926825</ref> <ref>PMID:12813056</ref> <ref>PMID:14604989</ref> <ref>PMID:15331714</ref> <ref>PMID:19438409</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/kp/2kpf_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/2kpf_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2kpf ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Specific interactions between transmembrane alpha-helices, to a large extent, determine the biological function of integral membrane proteins upon normal development and in pathological states of an organism. Various membrane-like media, partially those mimicking the conditions of multicomponent biological membranes, are used to study the structural and thermodynamic features that define the character of oligomerization of transmembrane helical segments. The choice of the composition of the membrane-mimicking medium is conducted in an effort to obtain a biologically relevant conformation of the protein complex and a sample that would be stable enough to allow to perform a series of long-term experiments with its use. In the present work, heteronuclear NMR spectroscopy and molecular dynamics simulations were used to demonstrate that the two most widely used media (detergent DPC micelles and lipid DMPC/DHPC bicelles) enable to perform structural studies of the specific interactions between transmembrane alpha-helices by the example of dimerizing the transmembrane domain of the bitopic protein glycophorin A. However, a number of peculiarities place lipid bicelles closer to natural lipid bilayers in terms of their physical properties.
-Dimeric structure of the transmembrane domain of glycophorin a in lipidic and detergent environments.,Mineev KS, Bocharov EV, Volynsky PE, Goncharuk MV, Tkach EN, Ermolyuk YS, Schulga AA, Chupin VV, Maslennikov IV, Efremov RG, Arseniev AS Acta Naturae. 2011 Apr;3(2):90-8. PMID:22649687<ref>PMID:22649687</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 27: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Arseniev, A S]]
+[[Category: Large Structures]]
-[[Category: Bocharov, E V]]
+[[Category: Arseniev AS]]
-[[Category: Efremov, R G]]
+[[Category: Bocharov EV]]
-[[Category: Goncharuk, M V]]
+[[Category: Efremov RG]]
-[[Category: Mineev, K S]]
+[[Category: Goncharuk MV]]
-[[Category: Volynsky, P E]]
+[[Category: Mineev KS]]
-[[Category: Bicelle]]
+[[Category: Volynsky PE]]
-[[Category: Blood group antigen]]
-[[Category: Cell membrane]]
-[[Category: Glycophorin some]]
-[[Category: Glycoprotein]]
-[[Category: Host-virus interaction]]
-[[Category: Membrane]]
-[[Category: Membrane protein]]
-[[Category: Micelle]]
-[[Category: Sialic acid]]
-[[Category: Transmembrane]]
-[[Category: Transmembrane dimer]]