1kb2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:55, 16 August 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1kb2.png|left|200px]]
 
-
<!--
+
==Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element==
-
The line below this paragraph, containing "STRUCTURE_1kb2", creates the "Structure Box" on the page.
+
<StructureSection load='1kb2' size='340' side='right'caption='[[1kb2]], [[Resolution|resolution]] 2.70&Aring;' 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'>[[1kb2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The November 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vitamin D Receptor'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_11 10.2210/rcsb_pdb/mom_2012_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KB2 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">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
{{STRUCTURE_1kb2| PDB=1kb2 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kb2 OCA], [https://pdbe.org/1kb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kb2 RCSB], [https://www.ebi.ac.uk/pdbsum/1kb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kb2 ProSAT]</span></td></tr>
 +
</table>
 +
== Disease ==
 +
[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[https://omim.org/entry/277440 277440]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:16252006</ref> <ref>PMID:10678179</ref> <ref>PMID:15728261</ref> <ref>PMID:16913708</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/kb/1kb2_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=1kb2 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The vitamin D receptor (VDR) forms homo- or heterodimers on response elements composed of two hexameric half-sites separated by 3 bp of spacer DNA. We describe here the crystal structures at 2.7-2.8 A resolution of the VDR DNA-binding region (DBD) in complex with response elements from three different promoters: osteopontin (SPP), canonical DR3 and osteocalcin (OC). These structures reveal the chemical basis for the increased affinity of VDR for the SPP response element, and for the poor stability of the VDR-OC complex, relative to the canonical DR3 response element. The homodimeric protein-protein interface is stabilized by van der Waals interactions and is predominantly non-polar. An extensive alpha-helix at the C-terminal end of the VDR DBD resembles that found in the thyroid hormone receptor (TR), and suggests a mechanism by which VDR and TR discriminate among response elements. Selective structure-based mutations in the asymmetric homodimeric interface result in a VDR DBD protein that is defective in homodimerization but now forms heterodimers with the 9-cis retinoic acid receptor (RXR) DBD.
-
===Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element===
+
Structural basis of VDR-DNA interactions on direct repeat response elements.,Shaffer PL, Gewirth DT EMBO J. 2002 May 1;21(9):2242-52. PMID:11980721<ref>PMID:11980721</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1kb2" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_11980721}}, adds the Publication Abstract to the page
+
*[[Sandbox vdr|Sandbox vdr]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 11980721 is the PubMed ID number.
+
*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
-
-->
+
== References ==
-
{{ABSTRACT_PUBMED_11980721}}
+
<references/>
-
 
+
__TOC__
-
==Disease==
+
</StructureSection>
-
Known disease associated with this structure: Osteoporosis, involutional, 166710 (1) OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601769 601769]], Rickets, vitamin D-resistant, type IIA OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601769 601769]]
+
-
 
+
-
==About this Structure==
+
-
1KB2 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KB2 OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:11980721</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Gewirth, D T.]]
+
[[Category: Large Structures]]
-
[[Category: Shaffer, P L.]]
+
[[Category: RCSB PDB Molecule of the Month]]
-
[[Category: Nuclear receptor]]
+
[[Category: Vitamin D Receptor]]
-
[[Category: Protein-dna complex]]
+
[[Category: Gewirth DT]]
-
[[Category: Vdr]]
+
[[Category: Shaffer PL]]
-
[[Category: Vitamin d]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:52:08 2009''
+

Current revision

Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element

PDB ID 1kb2

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/1kb2"
Personal tools