1j4w: Difference between revisions

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[[Image:1j4w.png|left|200px]]


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==COMPLEX OF THE KH3 and KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29mer DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE==
The line below this paragraph, containing "STRUCTURE_1j4w", creates the "Structure Box" on the page.
<StructureSection load='1j4w' size='340' side='right'caption='[[1j4w]]' 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'>[[1j4w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J4W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J4W 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">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j4w OCA], [https://pdbe.org/1j4w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j4w RCSB], [https://www.ebi.ac.uk/pdbsum/1j4w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j4w ProSAT]</span></td></tr>
{{STRUCTURE_1j4w|  PDB=1j4w  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/FUBP1_HUMAN FUBP1_HUMAN] Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.<ref>PMID:8125259</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/j4/1j4w_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=1j4w ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Gene regulation can be tightly controlled by recognition of DNA deformations that are induced by stress generated during transcription. The KH domains of the FUSE-binding protein (FBP), a regulator of c-myc expression, bind in vivo and in vitro to the single-stranded far-upstream element (FUSE), 1,500 base pairs upstream from the c-myc promoter. FBP bound to FUSE acts through TFIIH at the promoter. Here we report the solution structure of a complex between the KH3 and KH4 domains of FBP and a 29-base single-stranded DNA from FUSE. The KH domains recognize two sites, 9-10 bases in length, separated by 5 bases, with KH4 bound to the 5' site and KH3 to the 3' site. The central portion of each site comprises a tetrad of sequence 5'd-ATTC for KH4 and 5'd-TTTT for KH3. Dynamics measurements show that the two KH domains bind as articulated modules to single-stranded DNA, providing a flexible framework with which to recognize transient, moving targets.


===COMPLEX OF THE KH3 and KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29mer DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE===
Structure and dynamics of KH domains from FBP bound to single-stranded DNA.,Braddock DT, Louis JM, Baber JL, Levens D, Clore GM Nature. 2002 Feb 28;415(6875):1051-6. PMID:11875576<ref>PMID:11875576</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_11875576}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1j4w" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 11875576 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_11875576}}
__TOC__
 
</StructureSection>
==About this Structure==
1J4W is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J4W OCA].
 
==Reference==
Structure and dynamics of KH domains from FBP bound to single-stranded DNA., Braddock DT, Louis JM, Baber JL, Levens D, Clore GM, Nature. 2002 Feb 28;415(6875):1051-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11875576 11875576]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Braddock, D T.]]
[[Category: Braddock DT]]
[[Category: Clore, G M.]]
[[Category: Clore GM]]
[[Category: C-myc oncogene]]
[[Category: Fbp]]
[[Category: Fuse element]]
[[Category: Single-stranded dna binding protein]]
[[Category: Transcription factor]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 14:30:15 2008''

Latest revision as of 02:42, 28 December 2023

COMPLEX OF THE KH3 and KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29mer DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENECOMPLEX OF THE KH3 and KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29mer DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE

Structural highlights

1j4w is a 2 chain structure with sequence from Homo sapiens. 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

FUBP1_HUMAN Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.[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

Gene regulation can be tightly controlled by recognition of DNA deformations that are induced by stress generated during transcription. The KH domains of the FUSE-binding protein (FBP), a regulator of c-myc expression, bind in vivo and in vitro to the single-stranded far-upstream element (FUSE), 1,500 base pairs upstream from the c-myc promoter. FBP bound to FUSE acts through TFIIH at the promoter. Here we report the solution structure of a complex between the KH3 and KH4 domains of FBP and a 29-base single-stranded DNA from FUSE. The KH domains recognize two sites, 9-10 bases in length, separated by 5 bases, with KH4 bound to the 5' site and KH3 to the 3' site. The central portion of each site comprises a tetrad of sequence 5'd-ATTC for KH4 and 5'd-TTTT for KH3. Dynamics measurements show that the two KH domains bind as articulated modules to single-stranded DNA, providing a flexible framework with which to recognize transient, moving targets.

Structure and dynamics of KH domains from FBP bound to single-stranded DNA.,Braddock DT, Louis JM, Baber JL, Levens D, Clore GM Nature. 2002 Feb 28;415(6875):1051-6. PMID:11875576[2]

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

References

  1. ↑ Duncan R, Bazar L, Michelotti G, Tomonaga T, Krutzsch H, Avigan M, Levens D. A sequence-specific, single-strand binding protein activates the far upstream element of c-myc and defines a new DNA-binding motif. Genes Dev. 1994 Feb 15;8(4):465-80. PMID:8125259
  2. ↑ Braddock DT, Louis JM, Baber JL, Levens D, Clore GM. Structure and dynamics of KH domains from FBP bound to single-stranded DNA. Nature. 2002 Feb 28;415(6875):1051-6. PMID:11875576 doi:10.1038/4151051a
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