1zdk: Difference between revisions

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-{{Seed}}
-[[Image:1zdk.png|left|200px]]
-<!--
+==STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX==
-The line below this paragraph, containing "STRUCTURE_1zdk", creates the "Structure Box" on the page.
+<StructureSection load='1zdk' size='340' side='right'caption='[[1zdk]], [[Resolution|resolution]] 2.86&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'>[[1zdk]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_MS2 Escherichia phage MS2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZDK 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]] 2.86&#8491;</td></tr>
--->
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zdk OCA], [https://pdbe.org/1zdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zdk RCSB], [https://www.ebi.ac.uk/pdbsum/1zdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zdk ProSAT]</span></td></tr>
-{{STRUCTURE_1zdk|  PDB=1zdk  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CAPSD_BPMS2 CAPSD_BPMS2] Self-assembles to form the T=3 icosahedral virus shell that protects the viral nucleic acid. Acts as a translational repressor by binding with high specificity to a single stem-loop structure in the genomic RNA that contains the initiation codon of the gene for the viral replicase. Involved in virus assembly through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome.<ref>PMID:16531233</ref> <ref>PMID:18662904</ref> <ref>PMID:26608810</ref> <ref>PMID:8254664</ref> <ref>PMID:9245600</ref> <ref>PMID:9469847</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/zd/1zdk_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=1zdk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The coat protein of bacteriophage MS2 is known to bind specifically to an RNA hairpin formed within the MS2 genome. Structurally this hairpin is built up by an RNA double helix interrupted by one unpaired nucleotide and closed by a four-nucleotide loop. We have performed crystallographic studies of complexes between MS2 coat protein capsids and four RNA hairpin variants in order to evaluate the minimal requirements for tight binding to the coat protein and to obtain more information about the three-dimensional structure of these hairpins. An RNA fragment including the four loop nucleotides and a two-base-pair stem but without the unpaired nucleotide is sufficient for binding to the coat protein shell under the conditions used in this study. In contrast, an RNA fragment containing a stem with the unpaired nucleotide but missing the loop nucleotides does not bind to the protein shell.
-===STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX===
+Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements.,Grahn E, Stonehouse NJ, Murray JB, van den Worm S, Valegard K, Fridborg K, Stockley PG, Liljas L RNA. 1999 Jan;5(1):131-8. PMID:9917072<ref>PMID:9917072</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1zdk" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9917072}}, adds the Publication Abstract to the page
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9917072 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9917072}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia phage MS2]]
-ZDK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacterio_phage_ms2 Enterobacterio phage ms2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZDK OCA].
+[[Category: Large Structures]]
+[[Category: Grahn E]]
-==Reference==
+[[Category: Liljas L]]
-Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements., Grahn E, Stonehouse NJ, Murray JB, van den Worm S, Valegard K, Fridborg K, Stockley PG, Liljas L, RNA. 1999 Jan;5(1):131-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9917072 9917072]
+[[Category: Stonehouse NJ]]
-[[Category: Enterobacterio phage ms2]]
+[[Category: Valegard K]]
-[[Category: Single protein]]
+[[Category: Vandenworm S]]
-[[Category: Grahn, E.]]
-[[Category: Liljas, L.]]
-[[Category: Stonehouse, N J.]]
-[[Category: Valegard, K.]]
-[[Category: Vandenworm, S.]]
-[[Category: Coat protein]]
-[[Category: Icosahedral virus]]
-[[Category: Rna fragment]]
-[[Category: Rna-binding]]
-[[Category: Viral protein capsid]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 20:26:15 2008''