3bn4: Difference between revisions

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:3bn4.jpg|left|200px]]<br /><applet load="3bn4" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3bn4, resolution 2.000&Aring;" />
-'''Carboxysome Subunit, CcmK1'''<br />
-==Overview==
+==Carboxysome Subunit, CcmK1==
-The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.
+<StructureSection load='3bn4' size='340' side='right'caption='[[3bn4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[3bn4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. The June 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vaults''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_6 10.2210/rcsb_pdb/mom_2009_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BN4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BN4 FirstGlance]. <br>
-BN4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Sites: <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+E+123'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+C+123'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+A+123'>AC3</scene> and <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+B+123'>AC4</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BN4 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bn4 OCA], [https://pdbe.org/3bn4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bn4 RCSB], [https://www.ebi.ac.uk/pdbsum/3bn4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bn4 ProSAT]</span></td></tr>
-Atomic-level models of the bacterial carboxysome shell., Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, Yeates TO, Science. 2008 Feb 22;319(5866):1083-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18292340 18292340]
+</table>
-[[Category: Single protein]]
+== Function ==
-[[Category: Synechocystis sp.]]
+[https://www.uniprot.org/uniprot/CCMK1_SYNY3 CCMK1_SYNY3] May be involved in the formation of the carboxysome, a polyhedral inclusion where RuBisCO is sequestered (By similarity).
-[[Category: Sawaya, M R.]]
+== Evolutionary Conservation ==
-[[Category: Tanaka, S.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Yeates, T O.]]
+Check<jmol>
-[[Category: SO4]]
+  <jmolCheckbox>
-[[Category: hexamer]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bn/3bn4_consurf.spt"</scriptWhenChecked>
-[[Category: structural protein]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar  5 13:24:02 2008''
+  </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=3bn4 ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: RCSB PDB Molecule of the Month]]
+[[Category: Synechocystis sp]]
+[[Category: Vaults]]
+[[Category: Sawaya MR]]
+[[Category: Tanaka S]]
+[[Category: Yeates TO]]