2v1w: Difference between revisions
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== | ==Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1== | ||
<StructureSection load='2v1w' size='340' side='right'caption='[[2v1w]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2v1w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V1W FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=2v1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v1w OCA], [https://pdbe.org/2v1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v1w RCSB], [https://www.ebi.ac.uk/pdbsum/2v1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v1w ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PDLI4_HUMAN PDLI4_HUMAN] | |||
== 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/v1/2v1w_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=2v1w ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's "binding groove". We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the alpha B helix allow noncanonical binding interactions. These interactions may be indicative of intermediate states between unbound and fully bound PDZ domain and target protein. The noncanonical "perpendicular" binding observed potentially represents the general form of a kinetic intermediate. Comparison with canonical binding suggests that the rearrangement during binding involves both the PDZ domain and its ligand. | |||
Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms.,Elkins JM, Gileadi C, Shrestha L, Phillips C, Wang J, Muniz JR, Doyle DA Protein Sci. 2010 Apr;19(4):731-41. doi: 10.1002/pro.349. PMID:20120020<ref>PMID:20120020</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2v1w" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[PDZ and LIM domain protein|PDZ and LIM domain protein]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Arrowsmith | [[Category: Arrowsmith CH]] | ||
[[Category: Burgess-Brown | [[Category: Burgess-Brown N]] | ||
[[Category: Doyle D]] | |||
[[Category: Doyle | [[Category: Edwards A]] | ||
[[Category: Edwards | [[Category: Elkins J]] | ||
[[Category: Elkins | [[Category: Pike ACW]] | ||
[[Category: Pike | [[Category: Salah E]] | ||
[[Category: Salah | [[Category: Shrestha L]] | ||
[[Category: Shrestha | [[Category: Soundararajan M]] | ||
[[Category: Soundararajan | [[Category: Sundstrom M]] | ||
[[Category: Sundstrom | [[Category: Ugochukwu E]] | ||
[[Category: Ugochukwu | [[Category: Umeano C]] | ||
[[Category: Umeano | [[Category: Weigelt J]] | ||
[[Category: Weigelt | [[Category: Von Delft F]] | ||
[[Category: | |||
Latest revision as of 18:02, 13 December 2023
Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedPDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's "binding groove". We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the alpha B helix allow noncanonical binding interactions. These interactions may be indicative of intermediate states between unbound and fully bound PDZ domain and target protein. The noncanonical "perpendicular" binding observed potentially represents the general form of a kinetic intermediate. Comparison with canonical binding suggests that the rearrangement during binding involves both the PDZ domain and its ligand. Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms.,Elkins JM, Gileadi C, Shrestha L, Phillips C, Wang J, Muniz JR, Doyle DA Protein Sci. 2010 Apr;19(4):731-41. doi: 10.1002/pro.349. PMID:20120020[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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