1skn

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:31, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1skn.gif|left|200px]]
 
-
{{Structure
+
==THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF==
-
|PDB= 1skn |SIZE=350|CAPTION= <scene name='initialview01'>1skn</scene>, resolution 2.500&Aring;
+
<StructureSection load='1skn' size='340' side='right'caption='[[1skn]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>
+
<table><tr><td colspan='2'>[[1skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SKN FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
|GENE= SKN-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 Caenorhabditis elegans])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skn OCA], [https://pdbe.org/1skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1skn RCSB], [https://www.ebi.ac.uk/pdbsum/1skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1skn ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skn OCA], [http://www.ebi.ac.uk/pdbsum/1skn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1skn RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/SKN1_CAEEL SKN1_CAEEL] Required to specify the fate of ventral blastomeres in the early embryo, and postembryonically for the development of the intestine. Directly regulates expression of zygotically expressed med-1 and med-2 to direct mesendoderm development.<ref>PMID:1547503</ref> <ref>PMID:11463373</ref>
-
 
+
== Evolutionary Conservation ==
-
'''THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/1skn_consurf.spt"</scriptWhenChecked>
-
The DNA-binding domain of Skn-1, a developmental transcription factor that specifies mesoderm in C. elegans, is shown by X-ray crystallography to have a novel fold in which a compact, monomeric, four-helix unit organizes two DNA-contact elements. At the C-terminus, a helix extends from the domain to occupy the major groove of DNA in a manner similar to bZip proteins. Skn-1, however, lacks the leucine zipper found in all bZips. Additional contacts with the DNA are made by a short basic segment at the N-terminus of the domain, reminiscent of the 'homeodomain arm'.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1SKN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKN OCA].
+
</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=1skn ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
== References ==
-
A new DNA-binding motif in the Skn-1 binding domain-DNA complex., Rupert PB, Daughdrill GW, Bowerman B, Matthews BW, Nat Struct Biol. 1998 Jun;5(6):484-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9628487 9628487]
+
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Caenorhabditis elegans]]
[[Category: Caenorhabditis elegans]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Bowerman, B.]]
+
[[Category: Bowerman B]]
-
[[Category: Daughdrill, G W.]]
+
[[Category: Daughdrill GW]]
-
[[Category: Matthews, B W.]]
+
[[Category: Matthews BW]]
-
[[Category: Rupert, P B.]]
+
[[Category: Rupert PB]]
-
[[Category: complex (transcription factor/dna)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:43:18 2008''
+

Current revision

THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF

PDB ID 1skn

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1skn"
Personal tools