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.


1gcc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:21, 27 March 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1gcc.gif|left|200px]]
 
-
{{Structure
+
==SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE==
-
|PDB= 1gcc |SIZE=350|CAPTION= <scene name='initialview01'>1gcc</scene>
+
<StructureSection load='1gcc' size='340' side='right'caption='[[1gcc]]' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
+
<table><tr><td colspan='2'>[[1gcc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GCC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GCC FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
|GENE= ATERF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gcc OCA], [https://pdbe.org/1gcc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gcc RCSB], [https://www.ebi.ac.uk/pdbsum/1gcc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gcc ProSAT]</span></td></tr>
-
|DOMAIN=
+
</table>
-
|RELATEDENTRY=
+
== Function ==
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gcc OCA], [http://www.ebi.ac.uk/pdbsum/1gcc PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1gcc RCSB]</span>
+
[https://www.uniprot.org/uniprot/EF100_ARATH EF100_ARATH] Acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. Involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways.<ref>PMID:10715325</ref> <ref>PMID:11950980</ref> <ref>PMID:9756931</ref>
-
}}
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
'''SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE'''
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
 
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gc/1gcc_consurf.spt"</scriptWhenChecked>
-
==Overview==
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet.
+
<text>to colour the structure by Evolutionary Conservation</text>
-
 
+
</jmolCheckbox>
-
==About this Structure==
+
</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=1gcc ConSurf].
-
1GCC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GCC OCA].
+
<div style="clear:both"></div>
-
 
+
== References ==
-
==Reference==
+
<references/>
-
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA., Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M, EMBO J. 1998 Sep 15;17(18):5484-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9736626 9736626]
+
__TOC__
 +
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Allen, M D.]]
+
[[Category: Allen MD]]
-
[[Category: Ohme-Takagi, M.]]
+
[[Category: Ohme-Takagi M]]
-
[[Category: Suzuki, M.]]
+
[[Category: Suzuki M]]
-
[[Category: Tateno, M.]]
+
[[Category: Tateno M]]
-
[[Category: Yamasaki, K.]]
+
[[Category: Yamasaki K]]
-
[[Category: complex (transcription factor/dna)]]
+
-
[[Category: ethylene inducible]]
+
-
[[Category: protein-dna complex]]
+
-
[[Category: transcription factor]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:41:17 2008''
+

Current revision

SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE

PDB ID 1gcc

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/1gcc"
Personal tools