1w5t: Difference between revisions

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-{{Seed}}
-[[Image:1w5t.png|left|200px]]
-<!--
+==Structure of the Aeropyrum Pernix ORC2 protein (ADPNP-ADP complexes)==
-The line below this paragraph, containing "STRUCTURE_1w5t", creates the "Structure Box" on the page.
+<StructureSection load='1w5t' size='340' side='right'caption='[[1w5t]], [[Resolution|resolution]] 2.40&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'>[[1w5t]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W5T 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]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_1w5t|  PDB=1w5t  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1w5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w5t OCA], [https://pdbe.org/1w5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w5t RCSB], [https://www.ebi.ac.uk/pdbsum/1w5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w5t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CDC62_AERPE CDC62_AERPE] Involved in regulation of DNA replication (By similarity). Binds DNA.[HAMAP-Rule:MF_01407]<ref>PMID:15465044</ref>
+== 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/w5/1w5t_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=1w5t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Archaea contain one or more proteins with homology to eukaryotic ORC/Cdc6 proteins. Sequence analysis suggests the existence of at least two subfamilies of these proteins, for which we propose the nomenclature ORC1 and ORC2. We have determined crystal structures of the ORC2 protein from the archaeon Aeropyrum pernix in complexes with ADP or a non-hydrolysable ATP analogue, ADPNP. Between two crystal forms, there are three crystallographically independent views of the ADP complex and two of the ADPNP complex. The protein molecules in the three complexes with ADP adopt very different conformations, while the two complexes with ADPNP are the same. These structures indicate that there is considerable conformational flexibility in ORC2 but that ATP binding stabilises a single conformation. We show that the ORC2 protein can bind DNA, and that this activity is associated with the C-terminal domain of the protein. We present a model for the interaction of the winged helix (WH) domain of ORC2 with DNA that differs from that proposed previously for Pyrobaculum aerophilum ORC/Cdc6.
-===STRUCTURE OF THE AEROPYRUM PERNIX ORC2 PROTEIN (ADPNP-ADP COMPLEXES)===
+Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix.,Singleton MR, Morales R, Grainge I, Cook N, Isupov MN, Wigley DB J Mol Biol. 2004 Oct 22;343(3):547-57. PMID:15465044<ref>PMID:15465044</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15465044}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1w5t" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15465044 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15465044}}
+__TOC__
+</StructureSection>
-==About this Structure==
-W5T is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W5T OCA].
-==Reference==
-<ref group="xtra">PMID:15465044</ref><references group="xtra"/>
 [[Category: Aeropyrum pernix]]
-[[Category: Cook, N.]]
+[[Category: Large Structures]]
-[[Category: Grainge, I.]]
+[[Category: Cook N]]
-[[Category: Isupov, M N.]]
+[[Category: Grainge I]]
-[[Category: Morales, R.]]
+[[Category: Isupov MN]]
-[[Category: Singleton, M R.]]
+[[Category: Morales R]]
-[[Category: Wigley, D B.]]
+[[Category: Singleton MR]]
-[[Category: Aaa+ atpase]]
+[[Category: Wigley DB]]
-[[Category: Cdc6]]
-[[Category: Dna binding protein]]
-[[Category: Dna replication initiation]]
-[[Category: Orc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:15:51 2009''