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2vi6

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Revision as of 07:59, 25 June 2020

Crystal Structure of the Nanog Homeodomain

Structural highlights

2vi6 is a 8 chain structure with sequence from Lk3 transgenic mice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

The transcription factor Nanog is an upstream regulator in early mammalian development and a key determinant of pluripotency in embryonic stem cells. Nanog binds to promoter elements of hundreds of target genes and regulates their expression by an as yet unknown mechanism. Here, we report the crystal structure of the murine Nanog homeodomain (HD) and analysis of its interaction with a DNA element derived from the Tcf3 promoter. Two Nanog amino acid pairs, unique among HD sequences, appear to affect the mechanism of nonspecific DNA recognition as well as maintain the integrity of the structural scaffold. To assess selective DNA recognition by Nanog, we performed electrophoretic mobility shift assays using a panel of modified DNA binding sites and found that Nanog HD preferentially binds the TAAT(G/T)(G/T) motif. A series of rational mutagenesis experiments probing the role of six variant residues of Nanog on its DNA binding function establish their role in affecting binding affinity but not binding specificity. Together, the structural and functional evidence establish Nanog as a distant member of a Q50-type HD despite having considerable variation at the sequence level.

Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog.,Jauch R, Ng CK, Saikatendu KS, Stevens RC, Kolatkar PR J Mol Biol. 2008 Feb 22;376(3):758-70. Epub 2007 Dec 4. PMID:18177668^[1]

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

References

↑ Jauch R, Ng CK, Saikatendu KS, Stevens RC, Kolatkar PR. Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog. J Mol Biol. 2008 Feb 22;376(3):758-70. Epub 2007 Dec 4. PMID:18177668 doi:10.1016/j.jmb.2007.11.091

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vi6"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the Nanog Homeodomain==
-<StructureSection load='2vi6' size='340' side='right' caption='[[2vi6]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='2vi6' size='340' side='right'caption='[[2vi6]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vi6]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VI6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vi6]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VI6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VI6 FirstGlance]. <br>
-</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=2vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vi6 OCA], [http://pdbe.org/2vi6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vi6 RCSB], [http://www.ebi.ac.uk/pdbsum/2vi6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vi6 ProSAT]</span></td></tr>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vi6 OCA], [http://pdbe.org/2vi6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vi6 RCSB], [http://www.ebi.ac.uk/pdbsum/2vi6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vi6 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 29: / Line 29: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Lk3 transgenic mice]]
 [[Category: Jauch, R]]

2vi6

From Proteopedia

Revision as of 07:59, 25 June 2020

Crystal Structure of the Nanog Homeodomain

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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