3v4f: Difference between revisions

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<StructureSection load='3v4f' size='340' side='right'caption='[[3v4f]], [[Resolution|resolution]] 1.39&Aring;' scene=''>
<StructureSection load='3v4f' size='340' side='right'caption='[[3v4f]], [[Resolution|resolution]] 1.39&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3v4f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V4F FirstGlance]. <br>
<table><tr><td colspan='2'>[[3v4f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V4F FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTU:(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL'>DTU</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.391&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Hras, Hras1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTU:(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL'>DTU</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=3v4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v4f OCA], [https://pdbe.org/3v4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v4f RCSB], [https://www.ebi.ac.uk/pdbsum/3v4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v4f ProSAT]</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=3v4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v4f OCA], [https://pdbe.org/3v4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v4f RCSB], [https://www.ebi.ac.uk/pdbsum/3v4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v4f ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RASH_RAT RASH_RAT]] Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.  
[https://www.uniprot.org/uniprot/RASH_RAT RASH_RAT] Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the "on" state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the "ordered off" state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-beta. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.
 
Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition.,Holzapfel G, Buhrman G, Mattos C Biochemistry. 2012 Jul 30. PMID:22845804<ref>PMID:22845804</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3v4f" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[GTPase Hras 3D structures|GTPase Hras 3D structures]]
*[[GTPase Hras 3D structures|GTPase Hras 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Buffalo rat]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Holzapfel, G]]
[[Category: Rattus norvegicus]]
[[Category: Mattos, C]]
[[Category: Holzapfel G]]
[[Category: Gtp-binding]]
[[Category: Mattos C]]
[[Category: Nucleotide binding]]
[[Category: Signaling protein]]

Latest revision as of 13:31, 1 March 2024

H-Ras PEG 400/CaCl2, ordered offH-Ras PEG 400/CaCl2, ordered off

Structural highlights

3v4f is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.391Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RASH_RAT Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.

See Also

3v4f, resolution 1.39Å

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