2qto

From Proteopedia

(Difference between revisions)

Revision as of 11:31, 5 September 2018

An anisotropic model for potassium channel KcsA

Structural highlights

2qto is a 4 chain structure with sequence from "actinomyces_lividans"_krasil'nikov_et_al._1965 "actinomyces lividans" krasil'nikov et al. 1965. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1bl8
Gene:	kcsA, skc1 ("Actinomyces lividans" Krasil'nikov et al. 1965)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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(+).^[1]

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

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.

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^[2]

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

References

↑ Schrempf H, Schmidt O, Kummerlen R, Hinnah S, Muller D, Betzler M, Steinkamp T, Wagner R. A prokaryotic potassium ion channel with two predicted transmembrane segments from Streptomyces lividans. EMBO J. 1995 Nov 1;14(21):5170-8. PMID:7489706
↑ Chen X, Poon BK, Dousis A, Wang Q, Ma J. Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution. Structure. 2007 Aug;15(8):955-62. PMID:17698000 doi:10.1016/j.str.2007.06.012

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/2qto"

@@ Line 1: / Line 1: @@
 ==An anisotropic model for potassium channel KcsA==
 <StructureSection load='2qto' size='340' side='right' caption='[[2qto]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1bl8|1bl8]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kcsA, skc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1916 "Actinomyces lividans" Krasil'nikov et al. 1965])</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=2qto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qto OCA], [http://pdbe.org/2qto PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qto RCSB], [http://www.ebi.ac.uk/pdbsum/2qto PDBsum]</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=2qto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qto OCA], [http://pdbe.org/2qto PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qto RCSB], [http://www.ebi.ac.uk/pdbsum/2qto PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qto ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qt/2qto_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qt/2qto_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

2qto

From Proteopedia

Revision as of 11:31, 5 September 2018

An anisotropic model for potassium channel KcsA

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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