2qto

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[[Image:2qto.gif|left|200px]]
 
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{{Structure
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==An anisotropic model for potassium channel KcsA==
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|PDB= 2qto |SIZE=350|CAPTION= <scene name='initialview01'>2qto</scene>, resolution 3.201&Aring;
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<StructureSection load='2qto' size='340' side='right'caption='[[2qto]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>
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<table><tr><td colspan='2'>[[2qto]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QTO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QTO FirstGlance]. <br>
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|ACTIVITY=
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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]] 3.201&#8491;</td></tr>
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|GENE= kcsA, skc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1916 Streptomyces lividans])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
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|DOMAIN=
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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=2qto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qto OCA], [https://pdbe.org/2qto PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qto RCSB], [https://www.ebi.ac.uk/pdbsum/2qto PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qto ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1bl8|1BL8]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qto OCA], [http://www.ebi.ac.uk/pdbsum/2qto PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qto RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/KCSA_STRLI KCSA_STRLI] Acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, although it is not clear if this is the physiological stimulus for channel opening. Monovalent cation preference is K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+).<ref>PMID:7489706</ref>
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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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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qt/2qto_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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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=2qto ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We report a normal-mode method for anisotropic refinement of membrane-protein structures, based on a hypothesis that the global near-native-state disordering of membrane proteins in crystals follows low-frequency normal modes. Thus, a small set of modes is sufficient to represent the anisotropic thermal motions in X-ray crystallographic refinement. By applying the method to potassium channel KcsA at 3.2 A, we obtained a structural model with an improved fit with the diffraction data. Moreover, the improved electron density maps allowed for large structural adjustments for 12 residues in each subunit, including the rebuilding of 3 missing side chains. Overall, the anisotropic KcsA structure at 3.2 A was systematically closer to a 2.0 A KcsA structure, especially in the selectivity filter. Furthermore, the anisotropic thermal ellipsoids from the refinement revealed functionally relevant structural flexibility. We expect this method to be a valuable tool for structural refinement of many membrane proteins with moderate-resolution diffraction data.
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'''An anisotropic model for potassium channel KcsA'''
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Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution.,Chen X, Poon BK, Dousis A, Wang Q, Ma J Structure. 2007 Aug;15(8):955-62. PMID:17698000<ref>PMID:17698000</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2qto" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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We report a normal-mode method for anisotropic refinement of membrane-protein structures, based on a hypothesis that the global near-native-state disordering of membrane proteins in crystals follows low-frequency normal modes. Thus, a small set of modes is sufficient to represent the anisotropic thermal motions in X-ray crystallographic refinement. By applying the method to potassium channel KcsA at 3.2 A, we obtained a structural model with an improved fit with the diffraction data. Moreover, the improved electron density maps allowed for large structural adjustments for 12 residues in each subunit, including the rebuilding of 3 missing side chains. Overall, the anisotropic KcsA structure at 3.2 A was systematically closer to a 2.0 A KcsA structure, especially in the selectivity filter. Furthermore, the anisotropic thermal ellipsoids from the refinement revealed functionally relevant structural flexibility. We expect this method to be a valuable tool for structural refinement of many membrane proteins with moderate-resolution diffraction data.
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*[[Potassium channel 3D structures|Potassium channel 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2QTO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QTO OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution., Chen X, Poon BK, Dousis A, Wang Q, Ma J, Structure. 2007 Aug;15(8):955-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17698000 17698000]
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[[Category: Single protein]]
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[[Category: Streptomyces lividans]]
[[Category: Streptomyces lividans]]
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[[Category: Chen, X.]]
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[[Category: Chen X]]
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[[Category: Dousis, A.]]
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[[Category: Dousis A]]
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[[Category: Ma, J.]]
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[[Category: Ma J]]
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[[Category: Poon, B K.]]
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[[Category: Poon BK]]
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[[Category: Wang, Q.]]
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[[Category: Wang Q]]
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[[Category: anisotropic thermal factor]]
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[[Category: membrane protein]]
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[[Category: membrane protein]]
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[[Category: metal transport]]
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[[Category: normal-mode refinement]]
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[[Category: potassium channel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:53:09 2008''
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Current revision

An anisotropic model for potassium channel KcsA

PDB ID 2qto

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