3dn9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:50, 30 August 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3dn9.jpg|left|200px]]
 
-
<!--
+
==Carboxysome Subunit, CcmK1 C-terminal deletion mutant==
-
The line below this paragraph, containing "STRUCTURE_3dn9", creates the "Structure Box" on the page.
+
<StructureSection load='3dn9' size='340' side='right'caption='[[3dn9]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3dn9]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803 Synechocystis sp. PCC 6803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DN9 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28&#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>
-
{{STRUCTURE_3dn9| PDB=3dn9 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dn9 OCA], [https://pdbe.org/3dn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dn9 RCSB], [https://www.ebi.ac.uk/pdbsum/3dn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dn9 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[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).
 +
== 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/dn/3dn9_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=3dn9 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Carboxysomes are primitive bacterial organelles that function as a part of a carbon concentrating mechanism (CCM) under conditions where inorganic carbon is limiting. The carboxysome enhances the efficiency of cellular carbon fixation by encapsulating together carbonic anhydrase and the CO(2)-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). The carboxysome has a roughly icosahedral shape with an outer shell between 800 and 1500 A in diameter, which is constructed from a few thousand small protein subunits. In the cyanobacterium Synechocystis sp. PCC 6803, the previous structure determination of two homologous shell protein subunits, CcmK2 and CcmK4, elucidated how the outer shell is formed by the tight packing of CcmK hexamers into a molecular layer. Here we describe the crystal structure of the hexameric shell protein CcmK1, along with structures of mutants of both CcmK1 and CcmK2 lacking their sometimes flexible C-terminal tails. Variations in the way hexamers pack into layers are noted, while sulfate ions bound in pores through the layer provide further support for the hypothesis that the pores serve for transport of substrates and products into and out of the carboxysome. One of the new structures provides a high-resolution (1.3 A) framework for subsequent computational studies of molecular transport through the pores. Crystal and solution studies of the C-terminal deletion mutants demonstrate the tendency of the terminal segments to participate in protein--protein interactions, thereby providing a clue as to which side of the molecular layer of hexameric shell proteins is likely to face toward the carboxysome interior.
-
===Carboxysome Subunit, CcmK1 C-terminal deletion mutant===
+
Insights from multiple structures of the shell proteins from the beta-carboxysome.,Tanaka S, Sawaya MR, Phillips M, Yeates TO Protein Sci. 2009 Jan;18(1):108-20. PMID:19177356<ref>PMID:19177356</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
==About this Structure==
+
</div>
-
3DN9 is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DN9 OCA].
+
<div class="pdbe-citations 3dn9" style="background-color:#fffaf0;"></div>
-
[[Category: Synechocystis sp.]]
+
== References ==
-
[[Category: Sawaya, M R.]]
+
<references/>
-
[[Category: Tanaka, S.]]
+
__TOC__
-
[[Category: Yeates, T O.]]
+
</StructureSection>
-
[[Category: Hexamer]]
+
[[Category: Large Structures]]
-
[[Category: Structural protein]]
+
[[Category: Synechocystis sp. PCC 6803]]
-
 
+
[[Category: Sawaya MR]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 21 10:45:02 2009''
+
[[Category: Tanaka S]]
 +
[[Category: Yeates TO]]

Current revision

Carboxysome Subunit, CcmK1 C-terminal deletion mutant

PDB ID 3dn9

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools