3ig3: Difference between revisions

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<StructureSection load='3ig3' size='340' side='right'caption='[[3ig3]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
<StructureSection load='3ig3' size='340' side='right'caption='[[3ig3]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ig3]] is a 1 chain structure with sequence from [https://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=3IG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IG3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ig3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IG3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.99&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Plxna3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=3ig3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ig3 OCA], [https://pdbe.org/3ig3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ig3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ig3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ig3 ProSAT]</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=3ig3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ig3 OCA], [https://pdbe.org/3ig3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ig3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ig3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ig3 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PLXA3_MOUSE PLXA3_MOUSE]] Coreceptor for SEMA3A and SEMA3F. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Regulates the migration of sympathetic neurons, but not of neural crest precursors. Required for normal dendrite spine morphology in pyramidal neurons. May play a role in regulating semaphorin-mediated programmed cell death in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm.<ref>PMID:11683995</ref> <ref>PMID:18262512</ref> <ref>PMID:18804103</ref> <ref>PMID:19020035</ref> <ref>PMID:19717441</ref> <ref>PMID:20010807</ref>
[https://www.uniprot.org/uniprot/PLXA3_MOUSE PLXA3_MOUSE] Coreceptor for SEMA3A and SEMA3F. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Regulates the migration of sympathetic neurons, but not of neural crest precursors. Required for normal dendrite spine morphology in pyramidal neurons. May play a role in regulating semaphorin-mediated programmed cell death in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm.<ref>PMID:11683995</ref> <ref>PMID:18262512</ref> <ref>PMID:18804103</ref> <ref>PMID:19020035</ref> <ref>PMID:19717441</ref> <ref>PMID:20010807</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=3ig3 ConSurf].
</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=3ig3 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Plexin cell surface receptors bind to semaphorin ligands and transduce signals for regulating neuronal axon guidance. The intracellular region of plexins is essential for signaling and contains a R-Ras/M-Ras GTPase activating protein (GAP) domain that is divided into two segments by a Rho GTPase-binding domain (RBD). The regulation mechanisms for plexin remain elusive, although it is known that activation requires both binding of semaphorin to the extracellular region and a Rho-family GTPase (Rac1 or Rnd1) to the RBD. Here we report the crystal structure of the plexin A3 intracellular region. The structure shows that the N- and C-terminal portions of the GAP homologous regions together form a GAP domain with an overall fold similar to other Ras GAPs. However, the plexin GAP domain adopts a closed conformation and cannot accommodate R-Ras/M-Ras in its substrate-binding site, providing a structural basis for the autoinhibited state of plexins. A comparison with the plexin B1 RBD/Rnd1 complex structure suggests that Rnd1 binding alone does not induce a conformational change in plexin, explaining the requirement of both semaphorin and a Rho GTPase for activation. The structure also identifies an N-terminal segment that is important for regulation. Both the N-terminal segment and the RBD make extensive interactions with the GAP domain, suggesting the presence of an allosteric network connecting these three domains that integrates semaphorin and Rho GTPase signals to activate the GAP. The importance of these interactions in plexin signaling is shown by both cell-based and in vivo axon guidance assays.
Crystal structure of the plexin A3 intracellular region reveals an autoinhibited conformation through active site sequestration.,He H, Yang T, Terman JR, Zhang X Proc Natl Acad Sci U S A. 2009 Aug 26. PMID:19717441<ref>PMID:19717441</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ig3" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Plexin|Plexin]]
*[[Plexin 3D structures|Plexin 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lk3 transgenic mice]]
[[Category: Mus musculus]]
[[Category: He, H]]
[[Category: He H]]
[[Category: Zhang, X]]
[[Category: Zhang X]]
[[Category: Membrane]]
[[Category: Membrane protein]]
[[Category: Plexin intracellular gap rbd inactive]]
[[Category: Signaling protein]]
[[Category: Transmembrane]]

Latest revision as of 13:05, 21 February 2024

Crystal structure of mouse Plexin A3 intracellular domainCrystal structure of mouse Plexin A3 intracellular domain

Structural highlights

3ig3 is a 1 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.99Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PLXA3_MOUSE Coreceptor for SEMA3A and SEMA3F. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Regulates the migration of sympathetic neurons, but not of neural crest precursors. Required for normal dendrite spine morphology in pyramidal neurons. May play a role in regulating semaphorin-mediated programmed cell death in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm.[1] [2] [3] [4] [5] [6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Cheng HJ, Bagri A, Yaron A, Stein E, Pleasure SJ, Tessier-Lavigne M. Plexin-A3 mediates semaphorin signaling and regulates the development of hippocampal axonal projections. Neuron. 2001 Oct 25;32(2):249-63. PMID:11683995
  2. ↑ Waimey KE, Huang PH, Chen M, Cheng HJ. Plexin-A3 and plexin-A4 restrict the migration of sympathetic neurons but not their neural crest precursors. Dev Biol. 2008 Mar 15;315(2):448-58. doi: 10.1016/j.ydbio.2008.01.002. Epub 2008 , Jan 16. PMID:18262512 doi:http://dx.doi.org/10.1016/j.ydbio.2008.01.002
  3. ↑ Schwarz Q, Waimey KE, Golding M, Takamatsu H, Kumanogoh A, Fujisawa H, Cheng HJ, Ruhrberg C. Plexin A3 and plexin A4 convey semaphorin signals during facial nerve development. Dev Biol. 2008 Dec 1;324(1):1-9. doi: 10.1016/j.ydbio.2008.08.020. Epub 2008 Sep , 3. PMID:18804103 doi:http://dx.doi.org/10.1016/j.ydbio.2008.08.020
  4. ↑ Ben-Zvi A, Manor O, Schachner M, Yaron A, Tessier-Lavigne M, Behar O. The Semaphorin receptor PlexinA3 mediates neuronal apoptosis during dorsal root ganglia development. J Neurosci. 2008 Nov 19;28(47):12427-32. doi: 10.1523/JNEUROSCI.3573-08.2008. PMID:19020035 doi:http://dx.doi.org/10.1523/JNEUROSCI.3573-08.2008
  5. ↑ He H, Yang T, Terman JR, Zhang X. Crystal structure of the plexin A3 intracellular region reveals an autoinhibited conformation through active site sequestration. Proc Natl Acad Sci U S A. 2009 Aug 26. PMID:19717441
  6. ↑ Tran TS, Rubio ME, Clem RL, Johnson D, Case L, Tessier-Lavigne M, Huganir RL, Ginty DD, Kolodkin AL. Secreted semaphorins control spine distribution and morphogenesis in the postnatal CNS. Nature. 2009 Dec 24;462(7276):1065-9. doi: 10.1038/nature08628. Epub 2009 Dec 13. PMID:20010807 doi:http://dx.doi.org/10.1038/nature08628

3ig3, resolution 1.99Å

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