This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1dp7

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /> <applet load="1dp7" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dp7, resolution 1.5&Aring;" /> '''COCRYSTAL STRUCTURE ...)
Current revision (06:57, 7 February 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dp7.gif|left|200px]]<br />
 
-
<applet load="1dp7" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1dp7, resolution 1.5&Aring;" />
 
-
'''COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE'''<br />
 
-
==Overview==
+
==COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE==
-
Regulatory factor X (RFX) proteins are transcriptional activators that, recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N, is any nucleotide, R is a purine and Y is a pyrimidine) using a highly, conserved 76-residue DNA-binding domain (DBD). DNA-binding defects in the, protein RFX5 cause bare lymphocyte syndrome or major histocompatibility, antigen class II deficiency. RFX1, -2 and -3 regulate expression of other, medically important gene products (for example, interleukin-5 receptor, alpha chain, IL-5R alpha). Fusions of the ligand-binding domain of the, oestrogen receptor with the DBD of RFX4 occur in some human breast, tumours. Here we present a 1.5 A-resolution structure of two copies of the, DBD of human RFX1 (hRFX1) binding cooperatively to a symmetrical X-box., hRFX1 is an unusual member of the winged-helix subfamily of, helix-turn-helix proteins because it uses a beta-hairpin (or wing) to, recognize DNA instead of the recognition helix typical of helix-turn-helix, proteins. A new model for interactions between linker histones and DNA is, proposed.
+
<StructureSection load='1dp7' size='340' side='right'caption='[[1dp7]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1dp7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DP7 FirstGlance]. <br>
-
1DP7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with EDO and PEG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DP7 OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dp7 OCA], [https://pdbe.org/1dp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dp7 RCSB], [https://www.ebi.ac.uk/pdbsum/1dp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dp7 ProSAT]</span></td></tr>
-
Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding., Gajiwala KS, Chen H, Cornille F, Roques BP, Reith W, Mach B, Burley SK, Nature. 2000 Feb 24;403(6772):916-21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10706293 10706293]
+
</table>
-
[[Category: Single protein]]
+
== Function ==
-
[[Category: Burley, S.K.]]
+
[https://www.uniprot.org/uniprot/RFX1_HUMAN RFX1_HUMAN] Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.
-
[[Category: Chen, H.]]
+
== Evolutionary Conservation ==
-
[[Category: Cornille, F.]]
+
[[Image:Consurf_key_small.gif|200px|right]]
-
[[Category: Gajiwala, K.S.]]
+
Check<jmol>
-
[[Category: Mach, B.]]
+
<jmolCheckbox>
-
[[Category: Reith, W.]]
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/1dp7_consurf.spt"</scriptWhenChecked>
-
[[Category: Roques, B.P.]]
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
[[Category: EDO]]
+
<text>to colour the structure by Evolutionary Conservation</text>
-
[[Category: PEG]]
+
</jmolCheckbox>
-
[[Category: mhc class ii transcription factor]]
+
</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=1dp7 ConSurf].
-
[[Category: novel mode of dna recognition]]
+
<div style="clear:both"></div>
-
[[Category: protein-dna cocrystal structure]]
+
__TOC__
-
[[Category: winged helix]]
+
</StructureSection>
-
 
+
[[Category: Homo sapiens]]
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 16:34:38 2007''
+
[[Category: Large Structures]]
 +
[[Category: Burley SK]]
 +
[[Category: Chen H]]
 +
[[Category: Cornille F]]
 +
[[Category: Gajiwala KS]]
 +
[[Category: Mach B]]
 +
[[Category: Reith W]]
 +
[[Category: Roques BP]]

Current revision

COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE

PDB ID 1dp7

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/1dp7"
Personal tools