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.


2eqb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2eqb" size="450" color="white" frame="true" align="right" spinBox="true" caption="2eqb, resolution 2.70&Aring;" /> '''Crystal structure of...)
Current revision (13:50, 13 March 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2eqb.jpg|left|200px]]<br /><applet load="2eqb" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2eqb, resolution 2.70&Aring;" />
 
-
'''Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex'''<br />
 
-
==Overview==
+
==Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex==
-
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.
+
<StructureSection load='2eqb' size='340' side='right'caption='[[2eqb]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<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>
-
2EQB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with PO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2EQB 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]] 2.7&#8491;</td></tr>
-
 
+
<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>
-
==Reference==
+
<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>
-
Crystal structure of the Sec4p{middle dot}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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17488829 17488829]
+
</table>
-
[[Category: Protein 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 ==
 +
[[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/eq/2eqb_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=2eqb ConSurf].
 +
<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://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:05:33 2007''
+

Current revision

Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex

PDB ID 2eqb

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/2eqb"
Personal tools