2j46: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2j46.jpg|left|200px]]
- {{Structure
+==Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution==
-|PDB= 2j46 |SIZE=350|CAPTION= <scene name='initialview01'>2j46</scene>, resolution 1.135&Aring;
+<StructureSection load='2j46' size='340' side='right'caption='[[2j46]], [[Resolution|resolution]] 1.14&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>
+<table><tr><td colspan='2'>[[2j46]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J46 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.14&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j46 OCA], [https://pdbe.org/2j46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j46 RCSB], [https://www.ebi.ac.uk/pdbsum/2j46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j46 ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j46 OCA], [http://www.ebi.ac.uk/pdbsum/2j46 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2j46 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/SRP54_THEAQ SRP54_THEAQ] Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY (By similarity).[HAMAP-Rule:MF_00306]
+== 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/j4/2j46_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=2j46 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Two new structures of the SRP GTPase Ffh have been determined at 1.1 A resolution and provide the basis for comparative examination of the extensive water structure of the apo conformation of these GTPases. A set of well defined water-binding positions have been identified in the active site of the two-domain ;NG' GTPase, as well as at two functionally important interfaces. The water hydrogen-bonding network accommodates alternate conformations of the protein side chains by undergoing local rearrangements and, in one case, illustrates binding of a solute molecule within the active site by displacement of water molecules without further disruption of the water-interaction network. A subset of the water positions are well defined in several lower resolution structures, including those of different nucleotide-binding states; these appear to function in maintaining the protein structure. Consistent arrangements of surface water between three different ultrahigh-resolution structures provide a framework for beginning to understand how local water structure contributes to protein-ligand and protein-protein binding in the SRP GTPases.
-'''WATER STRUCTURE OF T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION'''
+Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh.,Ramirez UD, Freymann DM Acta Crystallogr D Biol Crystallogr. 2006 Dec;62(Pt 12):1520-34. Epub 2006, Nov 23. PMID:17139088<ref>PMID:17139088</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2j46" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Two new structures of the SRP GTPase Ffh have been determined at 1.1 A resolution and provide the basis for comparative examination of the extensive water structure of the apo conformation of these GTPases. A set of well defined water-binding positions have been identified in the active site of the two-domain ;NG' GTPase, as well as at two functionally important interfaces. The water hydrogen-bonding network accommodates alternate conformations of the protein side chains by undergoing local rearrangements and, in one case, illustrates binding of a solute molecule within the active site by displacement of water molecules without further disruption of the water-interaction network. A subset of the water positions are well defined in several lower resolution structures, including those of different nucleotide-binding states; these appear to function in maintaining the protein structure. Consistent arrangements of surface water between three different ultrahigh-resolution structures provide a framework for beginning to understand how local water structure contributes to protein-ligand and protein-protein binding in the SRP GTPases.
+*[[Signal recognition particle 3D structures|Signal recognition particle 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-J46 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J46 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh., Ramirez UD, Freymann DM, Acta Crystallogr D Biol Crystallogr. 2006 Dec;62(Pt 12):1520-34. Epub 2006, Nov 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17139088 17139088]
-[[Category: Single protein]]
 [[Category: Thermus aquaticus]]
-[[Category: Freymann, D M.]]
+[[Category: Freymann DM]]
-[[Category: Ramirez, U D.]]
+[[Category: Ramirez UD]]
-[[Category: ffh]]
-[[Category: gtp-binding]]
-[[Category: gtpase]]
-[[Category: nucleotide-binding]]
-[[Category: ribonucleoprotein]]
-[[Category: rna-binding]]
-[[Category: signal recognition particle]]
-[[Category: srp]]
-[[Category: water]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:52:41 2008''