2eqb: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2eqb.jpg|left|200px]]


{{Structure
==Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex==
|PDB= 2eqb |SIZE=350|CAPTION= <scene name='initialview01'>2eqb</scene>, resolution 2.70&Aring;
<StructureSection load='2eqb' size='340' side='right'caption='[[2eqb]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE ION'>PO4</scene>
<table><tr><td colspan='2'>[[2eqb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EQB FirstGlance]. <br>
|ACTIVITY=  
</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>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2eqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eqb OCA], [https://pdbe.org/2eqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eqb RCSB], [https://www.ebi.ac.uk/pdbsum/2eqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eqb ProSAT]</span></td></tr>
 
</table>
'''Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex'''
== Function ==
 
[https://www.uniprot.org/uniprot/SEC4_YEAST SEC4_YEAST] Involved in exocytosis. Maybe by regulating the binding and fusion of secretory vesicles with the cell surface. The GTP-bound form of SEC4 may interact with an effector, thereby stimulating its activity and leading to exocytotic fusion. SEC4 may be an upstream activator of the 19.5S SEC8/SEC15 particle. SEC4 probably interacts directly with SEC8; it could serve as the attachment site for the SEC8/SEC15 particle.<ref>PMID:16390997</ref>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
Vesicular transport during exocytosis is regulated by Rab GTPase (Sec4p in yeast), which is activated by a guanine nucleotide exchange factor (GEF) called Sec2p. Here, we report the crystal structure of the Sec2p GEF domain in a complex with the nucleotide-free Sec4p at 2.7 A resolution. Upon complex formation, the Sec2p helices approach each other, flipping the side chain of Phe-109 toward Leu-104 and Leu-108 of Sec2p. These three residues provide a hydrophobic platform to attract the side chains of Phe-49, Ile-53, and Ile-55 in the switch I region as well as Phe-57 and Trp-74 in the interswitch region of Sec4p. Consequently, the switch I and II regions are largely deformed, to create a flat hydrophobic interface that snugly fits the surface of the Sec2p coiled coil. These drastic conformational changes disrupt the interactions between switch I and the bound guanine nucleotide, which facilitates the GDP release. Unlike the recently reported 3.3 A structure of the Sec4p.Sec2p complex, our structure contains a phosphate ion bound to the P-loop, which may represent an intermediate state of the nucleotide exchange reaction.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eq/2eqb_consurf.spt"</scriptWhenChecked>
2EQB is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EQB OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Crystal structure of the Sec4p.Sec2p complex in the nucleotide exchanging intermediate state., Sato Y, Fukai S, Ishitani R, Nureki O, Proc Natl Acad Sci U S A. 2007 May 15;104(20):8305-10. Epub 2007 May 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17488829 17488829]
</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=2eqb ConSurf].
[[Category: Protein complex]]
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Fukai, S.]]
[[Category: Fukai S]]
[[Category: Ishitani, R.]]
[[Category: Ishitani R]]
[[Category: Nureki, O.]]
[[Category: Nureki O]]
[[Category: Sato, Y.]]
[[Category: Sato Y]]
[[Category: PO4]]
[[Category: coiled coil]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:43:17 2008''
Retrieved from "https://proteopedia.org/2eqb"