2hdc

From Proteopedia

(Difference between revisions)

Current revision

STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX

Structural highlights

2hdc is a 3 chain structure with sequence from Rattus norvegicus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FOXD3_RAT Binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3' and acts as a transcriptional repressor. Also acts as a transcriptional activator. Promotes development of neural crest cells from neural tube progenitors. Restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. Required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Genesis is an HNF-3/fkh homologous protein. By using multi-dimensional NMR techniques, we have obtained the solution structure and backbone dynamics of Genesis complexed with a 17 base-pair DNA. Our results indicate that both the local folding and dynamic properties of Genesis are perturbed when it binds to the DNA site. Our data show that a conserved flexible amino acid sequence (wing 1) makes dynamic contacts to DNA in the complex and a short helix is induced by Genesis-DNA interactions. Our data indicate that, unlike the HNF-3gamma/DNA complex, a magnesium ion is not required in forming the stable Genesis-DNA complex.

Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex.,Jin C, Marsden I, Chen X, Liao X J Mol Biol. 1999 Jun 18;289(4):683-90. PMID:10369754^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jin C, Marsden I, Chen X, Liao X. Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex. J Mol Biol. 1999 Jun 18;289(4):683-90. PMID:10369754 doi:10.1006/jmbi.1999.2819

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2hdc"

@@ Line 1: / Line 1: @@
 ==STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX==
-<StructureSection load='2hdc' size='340' side='right' caption='[[2hdc]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2hdc' size='340' side='right'caption='[[2hdc]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2hdc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HDC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2hdc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HDC FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GENESIS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>
+</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hdc RCSB], [http://www.ebi.ac.uk/pdbsum/2hdc PDBsum]</span></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=2hdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdc OCA], [https://pdbe.org/2hdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hdc RCSB], [https://www.ebi.ac.uk/pdbsum/2hdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/FOXD3_RAT FOXD3_RAT]] Binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3' and acts as a transcriptional repressor. Also acts as a transcriptional activator. Promotes development of neural crest cells from neural tube progenitors. Restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. Required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis (By similarity).
+[https://www.uniprot.org/uniprot/FOXD3_RAT FOXD3_RAT] Binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3' and acts as a transcriptional repressor. Also acts as a transcriptional activator. Promotes development of neural crest cells from neural tube progenitors. Restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. Required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis (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/hd/2hdc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hd/2hdc_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2hdc ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2hdc" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Rattus norvegicus]]
-[[Category: Chen, X]]
+[[Category: Chen X]]
-[[Category: Jin, C]]
+[[Category: Jin C]]
-[[Category: Liao, X]]
+[[Category: Liao X]]
-[[Category: Marsden, I]]
+[[Category: Marsden I]]
-[[Category: Dyanamic]]
-[[Category: Genesis]]
-[[Category: Protein-dna complex]]
-[[Category: Winged helix protein]]

2hdc

From Proteopedia

Current revision

STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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