1ity: 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: @@
-{{Seed}}
-[[Image:1ity.png|left|200px]]
-<!--
+==Solution structure of the DNA binding domain of human TRF1==
-The line below this paragraph, containing "STRUCTURE_1ity", creates the "Structure Box" on the page.
+<StructureSection load='1ity' size='340' side='right'caption='[[1ity]]' 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'>[[1ity]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ITY 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">Solution NMR</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=1ity FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ity OCA], [https://pdbe.org/1ity PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ity RCSB], [https://www.ebi.ac.uk/pdbsum/1ity PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ity ProSAT], [https://www.topsan.org/Proteins/RSGI/1ity TOPSAN]</span></td></tr>
-{{STRUCTURE_1ity|  PDB=1ity  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TERF1_HUMAN TERF1_HUMAN] Binds the telomeric double-stranded TTAGGG repeat and negatively regulates telomere length. Involved in the regulation of the mitotic spindle. Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double-stranded TTAGGG repeats added by telomerase and protects chromosome ends; without its protective activity, telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways.<ref>PMID:16166375</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/it/1ity_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=1ity ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Mammalian telomeres consist of long tandem arrays of double-stranded TTAGGG sequence motif packaged by TRF1 and TRF2. In contrast to the DNA binding domain of c-Myb, which consists of three imperfect tandem repeats, DNA binding domains of both TRF1 and TRF2 contain only a single Myb repeat. In a DNA complex of c-Myb, both the second and third repeats are closely packed in the major groove of DNA and recognize a specific base sequence cooperatively. RESULTS: The structure of the DNA binding domain of human TRF1 bound to telomeric DNA has been determined by NMR. It consists of three helices, whose architecture is very close to that of three repeats of the c-Myb DNA binding domain. Only the single Myb domain of TRF1 is sufficient for the sequence-specific recognition. The third helix of TRF1 recognizes the TAGGG part in the major groove, and the N-terminal arm interacts with the TT part in the minor groove. CONCLUSIONS: The DNA binding domain of TRF1 can specifically and fully recognize the AGGGTT sequence. It is likely that, in the dimer of TRF1, two DNA binding domains can bind independently in tandem arrays to two binding sites of telomeric DNA that is composed of the repeated AGGGTT motif. Although TRF2 plays an important role in the t loop formation that protects the ends of telomeres, it is likely that the binding mode of TRF2 to double-stranded telomeric DNA is almost identical to that of TRF1.
-===Solution structure of the DNA binding domain of human TRF1===
+Solution structure of a telomeric DNA complex of human TRF1.,Nishikawa T, Okamura H, Nagadoi A, Konig P, Rhodes D, Nishimura Y Structure. 2001 Dec;9(12):1237-51. PMID:11738049<ref>PMID:11738049</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_11738049}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ity" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11738049 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11738049}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ITY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITY OCA].
-==Reference==
-Solution structure of a telomeric DNA complex of human TRF1., Nishikawa T, Okamura H, Nagadoi A, Konig P, Rhodes D, Nishimura Y, Structure. 2001 Dec;9(12):1237-51. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11738049 11738049]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Konig, P.]]
+[[Category: Konig P]]
-[[Category: Nagadoi, A.]]
+[[Category: Nagadoi A]]
-[[Category: Nishikawa, T.]]
+[[Category: Nishikawa T]]
-[[Category: Nishimura, Y.]]
+[[Category: Nishimura Y]]
-[[Category: Okamura, H.]]
+[[Category: Okamura H]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Rhodes D]]
-[[Category: Rhodes, D.]]
-[[Category: Dna binding]]
-[[Category: Helix-turn-helix]]
-[[Category: Myb domain]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: Telomere]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 13:59:32 2008''