5xwt: Difference between revisions

Latest revision as of 07:45, 17 October 2024

Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig

Structural highlights

5xwt is a 4 chain structure with sequence from Homo sapiens and Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 4.178Å
Ligands:	NAG, PRD_900017
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PTPRD_MOUSE

Publication Abstract from PubMed

Synapse formation is triggered by trans-synaptic interactions of cell adhesion molecules, termed synaptic organizers. Three members of type-II receptor protein tyrosine phosphatases (classified as type-IIa RPTPs; PTPdelta, PTPsigma and LAR) are known as presynaptic organizers. Synaptic adhesion-like molecules (SALMs) have recently emerged as a family of postsynaptic organizers. Although all five SALM isoforms can bind to the type-IIa RPTPs, only SALM3 and SALM5 reportedly have synaptogenic activities depending on their binding. Here, we report the crystal structures of apo-SALM5, and PTPdelta-SALM2 and PTPdelta-SALM5 complexes. The leucine-rich repeat (LRR) domains of SALMs interact with the second immunoglobulin-like (Ig) domain of PTPdelta, whereas the Ig domains of SALMs interact with both the second and third Ig domains of PTPdelta. Unexpectedly, the structures exhibit the LRR-mediated 2:2 complex. Our synaptogenic co-culture assay using site-directed SALM5 mutants demonstrates that presynaptic differentiation induced by PTPdelta-SALM5 requires the dimeric property of SALM5.

Structural basis of trans-synaptic interactions between PTPdelta and SALMs for inducing synapse formation.,Goto-Ito S, Yamagata A, Sato Y, Uemura T, Shiroshima T, Maeda A, Imai A, Mori H, Yoshida T, Fukai S Nat Commun. 2018 Jan 18;9(1):269. doi: 10.1038/s41467-017-02417-z. PMID:29348429^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Goto-Ito S, Yamagata A, Sato Y, Uemura T, Shiroshima T, Maeda A, Imai A, Mori H, Yoshida T, Fukai S. Structural basis of trans-synaptic interactions between PTPdelta and SALMs for inducing synapse formation. Nat Commun. 2018 Jan 18;9(1):269. doi: 10.1038/s41467-017-02417-z. PMID:29348429 doi:https://dx.doi.org/10.1038/s41467-017-02417-z

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OCA

[1] Goto-Ito S, Yamagata A, Sato Y, Uemura T, Shiroshima T, Maeda A, Imai A, Mori H, Yoshida T, Fukai S. Structural basis of trans-synaptic interactions between PTPdelta and SALMs for inducing synapse formation. Nat Commun. 2018 Jan 18;9(1):269. doi: 10.1038/s41467-017-02417-z. PMID:29348429 doi:https://dx.doi.org/10.1038/s41467-017-02417-z

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5xwt' size='340' side='right'caption='[[5xwt]], [[Resolution|resolution]] 4.18&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xwt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XWT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XWT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xwt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=5XWT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XWT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 4.178&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ptprd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), LRFN5, C14orf146, SALM5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900017:triacetyl-beta-chitotriose'>PRD_900017</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=5xwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xwt OCA], [https://pdbe.org/5xwt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xwt RCSB], [https://www.ebi.ac.uk/pdbsum/5xwt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xwt ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xwt OCA], [http://pdbe.org/5xwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xwt RCSB], [http://www.ebi.ac.uk/pdbsum/5xwt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xwt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LRFN5_HUMAN LRFN5_HUMAN]] Cell adhesion molecule that mediates homophilic cell-cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons.<ref>PMID:18227064</ref> <ref>PMID:18585462</ref>
+[https://www.uniprot.org/uniprot/PTPRD_MOUSE PTPRD_MOUSE]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 ==See Also==
+*[[Tubulin tyrosine ligase 3D structures|Tubulin tyrosine ligase 3D structures]]
 *[[Tyrosine phosphatase 3D structures|Tyrosine phosphatase 3D structures]]
 == References ==
@@ Line 27: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Protein-tyrosine-phosphatase]]
+[[Category: Fukai S]]
-[[Category: Fukai, S]]
+[[Category: Goto-Ito S]]
-[[Category: Goto-Ito, S]]
+[[Category: Sato Y]]
-[[Category: Sato, Y]]
+[[Category: Yamagata A]]
-[[Category: Yamagata, A]]
-[[Category: Cell adhesion]]
-[[Category: Synaptic orgnizer]]

5xwt: Difference between revisions

Latest revision as of 07:45, 17 October 2024

Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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