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.


1sem

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:31, 1 May 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1sem.jpg|left|200px]]
 
-
{{Structure
+
==STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS==
-
|PDB= 1sem |SIZE=350|CAPTION= <scene name='initialview01'>1sem</scene>, resolution 2.0&Aring;
+
<StructureSection load='1sem' size='340' side='right'caption='[[1sem]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>
+
<table><tr><td colspan='2'>[[1sem]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SEM 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&#8491;</td></tr>
-
|GENE= GRB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 Caenorhabditis elegans])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sem OCA], [https://pdbe.org/1sem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sem RCSB], [https://www.ebi.ac.uk/pdbsum/1sem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sem ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sem OCA], [http://www.ebi.ac.uk/pdbsum/1sem PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1sem RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/SEM5_CAEEL SEM5_CAEEL] Acts both in vulval induction and sex myoblast migration. Presumably interacts with the kinase receptor let-23 and with a target that modifies the Ras-like protein let-60.
-
 
+
== Evolutionary Conservation ==
-
'''STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/se/1sem_consurf.spt"</scriptWhenChecked>
-
The Src-homology-3 (SH3) domains of the Caenorhabditis elegans protein SEM-5 and its human and Drosophila homologues, Grb2 and Drk (refs 1-4), bind proline-rich sequences found in the nucleotide-exchange factor Sos as part of their proposed function linking receptor tyrosine kinase activation to Ras activation. Here we report the crystal structure at 2.0 A resolution of the carboxy-terminal SH3 domain from SEM-5 complexed to the mSos-derived amino-acid sequence PPPVPPRRR. The peptide is found to bind in an orientation ('minus') that is precisely opposite to that observed previously ('plus' orientation) in other SH3-peptide complexes. This novel ability of peptide-recognition proteins to recognize peptides in two distinct modes may play an important role in the signalling specificity of pathways involving SH3 domains. Comparison of this structure with other SH3 complexes reveals how a conserved binding face can be used to recognize peptides in different orientations, and why the Sos peptide binds in this particular orientation.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1SEM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SEM OCA].
+
</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=1sem ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
__TOC__
-
Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains., Lim WA, Richards FM, Fox RO, Nature. 1994 Nov 24;372(6504):375-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7802869 7802869]
+
</StructureSection>
[[Category: Caenorhabditis elegans]]
[[Category: Caenorhabditis elegans]]
 +
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
-
[[Category: Single protein]]
+
[[Category: Fox RO]]
-
[[Category: Fox, R O.]]
+
[[Category: Lim WA]]
-
[[Category: Lim, W A.]]
+
[[Category: Richards FM]]
-
[[Category: Richards, F M.]]
+
-
[[Category: guanine nucleotide exchange factor]]
+
-
[[Category: peptide-binding protein]]
+
-
[[Category: src-homology 3 (sh3) domain]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:40:58 2008''
+

Current revision

STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS

PDB ID 1sem

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/1sem"
Personal tools