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1i11

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SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE

Structural highlights

1i11 is a 1 chain structure with sequence from Mus musculus. 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

SOX5_MOUSE Binds specifically to the DNA sequence 5'-AACAAT-3'. Activates transcription of COL2A1 and AGC1 in vitro.^[1]

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 fold of the murine Sox-5 (mSox-5) HMG box in free solution has been determined by multidimensional NMR using (15)N-labeled protein and has been found to adopt the characteristic twisted L-shape made up of two wings: the major wing comprising helix 1 (F10--F25) and helix 2 (N32--A43), the minor wing comprising helix 3 (P51--Y67) in weak antiparallel association with the N-terminal extended segment. (15)N relaxation measurements show considerable mobility (reduced order parameter, S(2)) in the minor wing that increases toward the amino and carboxy termini of the chain. The mobility of residues C-terminal to Q62 is significantly greater than the equivalent residues of non-sequence-specific boxes, and these residues show a weaker association with the extended N-terminal segment than in non-sequence boxes. Comparison with previously determined structures of HMG boxes both in free solution and complexed with DNA shows close similarity in the packing of the hydrophobic cores and the relative disposition of the three helices. Only in hSRY/DNA does the arrangement of aromatic sidechains differ significantly from that of mSox-5, and only in rHMG1 box 1 bound to cisplatinated DNA does helix 1 have no kink. Helix 3 in mSox-5 is terminated by P68, a conserved residue in DNA sequence-specific HMG boxes, which results in the chain turning through approximately 90 degrees.

Solution structure and backbone dynamics of the DNA-binding domain of mouse Sox-5.,Cary PD, Read CM, Davis B, Driscoll PC, Crane-Robinson C Protein Sci. 2001 Jan;10(1):83-98. PMID:11266597^[2]

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

References

↑ Lefebvre V, Li P, de Crombrugghe B. A new long form of Sox5 (L-Sox5), Sox6 and Sox9 are coexpressed in chondrogenesis and cooperatively activate the type II collagen gene. EMBO J. 1998 Oct 1;17(19):5718-33. PMID:9755172 doi:http://dx.doi.org/10.1093/emboj/17.19.5718
↑ Cary PD, Read CM, Davis B, Driscoll PC, Crane-Robinson C. Solution structure and backbone dynamics of the DNA-binding domain of mouse Sox-5. Protein Sci. 2001 Jan;10(1):83-98. PMID:11266597

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/1i11"

@@ Line 1: / Line 1: @@
 ==SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE==
-<StructureSection load='1i11' size='340' side='right' caption='[[1i11]], [[NMR_Ensembles_of_Models | 30 NMR models]]' scene=''>
+<StructureSection load='1i11' size='340' side='right'caption='[[1i11]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1i11]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1I11 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1i11]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I11 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SOX-5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=1i11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i11 OCA], [http://pdbe.org/1i11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1i11 RCSB], [http://www.ebi.ac.uk/pdbsum/1i11 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=1i11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i11 OCA], [https://pdbe.org/1i11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i11 RCSB], [https://www.ebi.ac.uk/pdbsum/1i11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i11 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SOX5_MOUSE SOX5_MOUSE]] Binds specifically to the DNA sequence 5'-AACAAT-3'. Activates transcription of COL2A1 and AGC1 in vitro.<ref>PMID:9755172</ref>
+[https://www.uniprot.org/uniprot/SOX5_MOUSE SOX5_MOUSE] Binds specifically to the DNA sequence 5'-AACAAT-3'. Activates transcription of COL2A1 and AGC1 in vitro.<ref>PMID:9755172</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/i1/1i11_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i1/1i11_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Lk3 transgenic mice]]
+[[Category: Large Structures]]
-[[Category: Cary, P D]]
+[[Category: Mus musculus]]
-[[Category: Crane-Robinson, C]]
+[[Category: Cary PD]]
-[[Category: Davis, B]]
+[[Category: Crane-Robinson C]]
-[[Category: Driscoll, P C]]
+[[Category: Davis B]]
-[[Category: Read, C M]]
+[[Category: Driscoll PC]]
-[[Category: Chromatin]]
+[[Category: Read CM]]
-[[Category: Dna bending]]
-[[Category: Dna binding protein]]
-[[Category: Dna recognition]]
-[[Category: Dna sequence specific]]
-[[Category: Hmg box]]
-[[Category: Testis determining]]

1i11

From Proteopedia

Current revision

SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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