Sandbox Reserved 1093: Difference between revisions

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== Structural highlights ==

~~This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.~~

~~You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.~~

The X-ray structure of ~~<Structure load='LRRTM2' size='350' frame='true' align='right' caption='Insert caption here' scene='~~LRRTM2~~<scene name='82/829346/Lrrtm2/1'>Text To Be Displayed</scene>' />~~ reveals that this transmembrane protein is composed of 3 main domains: a N-terminal leucine rich repeat domain which is extracellular, a single transmembrane domain and a C-terminal cytoplasmic region. The protein is composed of 516 amino acids.

The X-ray structure of LRRTM2 reveals that this transmembrane protein is composed of 3 main domains: a N-terminal leucine rich repeat domain which is extracellular, a single transmembrane domain and a C-terminal cytoplasmic region. The protein is composed of 516 amino acids.

1) <scene name='82/829346/Lrrtm2/3'>N-term fixation domain</scene>

~~1) N-term fixation domain~~

The N-terminal signal peptide is long of 33 amino. The extracellular domain contains 399 amino acids organized in 2 cysteine-rich domains (<scene name='82/829346/Lrrnt/1'>LRRNT</scene> and <scene name='82/829346/Lrrct/1'>LRRCT</scene>) and <scene name='82/829346/Lrr/2'>10 leucine rich domains</scene> (LRR). Each LRR domain is composed of 21 amino acids containing the conserved 11-aa sequence, LxxLxLxxN/ CxL, where x is any amino acid, and <scene name='82/829346/Lrr/1'>leucines</scene> and asparagine can be replaced with other hydrophobic residues. The leucine rich repeat domain forms a convex structure stabilized by a <scene name='82/829346/Lrr/1'>Phe</scene> spine. The concave surface is composed of a continuous <scene name='82/829346/Beta_sheets/1'>β-sheet</scene>, which provides an effective ligand-binding site, whereas the convex surface consists of <scene name='82/829346/Alpha_helix/1'>α-helices</scene>, which affect the curvature of the LRR domain.

The N-terminal signal peptide is long of 33 amino. The extracellular domain contains 399 amino acids organized in 2 cysteine-rich domains (LRRNT and LRRCT) and 10 leucine rich domains (LRR). Each LRR domain is composed of 21 amino acids containing the conserved 11-aa sequence, LxxLxLxxN/ CxL, where x is any amino acid, and leucines and asparagine can be replaced with other hydrophobic residues. The leucine rich repeat domain forms a convex structure stabilized by a Phe spine. The concave surface is composed of a continuous β-sheet, which provides an effective ligand-binding site, whereas the convex surface consists of α-helices, which affect the curvature of the LRR domain.

The N-terminal domain allows for the fixation of Nrxns which binds to the concave surface of the LRR1-LRR5 part of the protein. This fixation is mediated by calcium ions which interacts with the Asp144 and Asp212 of LRRTMT2. It was also observed that LRRTM2 Glu348 interacts with Ca2+ through a water molecule. In top of the Ca2+ mediated interaction, there is the formation of a hydrogen bound between the Asp352 of LRRTM2 and the Arg206 of Nrxns as well as hydrophobic interactions between the LRRTM2 Phe357 and Nrxns Leu208.

The fixation of Nrxns doesn’t change the conformation of the protein aside from Glu348 flipping toward the calcium ions.

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3) C-term fixation domain

The cytoplasmic domain contains 73 amino acids. It has been shown that the deletion of 55 residues from the C-terminal domain leads to abnormal intracellular trafficking pathway. This results in LRRTM2 being present in everywhere in the cell. This domain also contains a PSD consensus cytoplasmic binding domain (ECEV) which binds PSD-95 (postsynaptic scaffolding protein)

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

Sandbox Reserved 1093: Difference between revisions

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@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
-This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
-The X-ray structure of <Structure load='LRRTM2' size='350' frame='true' align='right' caption='Insert caption here' scene='LRRTM2<scene name='82/829346/Lrrtm2/1'>Text To Be Displayed</scene>' /> reveals that this transmembrane protein is composed of 3 main domains: a N-terminal leucine rich repeat domain which is extracellular, a single transmembrane domain and a C-terminal cytoplasmic region. The protein is composed of 516 amino acids.
+The X-ray structure of LRRTM2 reveals that this transmembrane protein is composed of 3 main domains: a N-terminal leucine rich repeat domain which is extracellular, a single transmembrane domain and a C-terminal cytoplasmic region. The protein is composed of 516 amino acids.
+)	<scene name='82/829346/Lrrtm2/3'>N-term fixation domain</scene>
-)	N-term fixation domain
+The N-terminal signal peptide is long of 33 amino. The extracellular domain contains 399 amino acids organized in 2 cysteine-rich domains (<scene name='82/829346/Lrrnt/1'>LRRNT</scene> and <scene name='82/829346/Lrrct/1'>LRRCT</scene>) and <scene name='82/829346/Lrr/2'>10 leucine rich domains</scene> (LRR). Each LRR domain is composed of 21 amino acids containing the conserved 11-aa sequence, LxxLxLxxN/ CxL, where x is any amino acid, and <scene name='82/829346/Lrr/1'>leucines</scene> and asparagine can be replaced with other hydrophobic residues. The leucine rich repeat domain forms a convex structure stabilized by a <scene name='82/829346/Lrr/1'>Phe</scene> spine. The concave surface is composed of a continuous <scene name='82/829346/Beta_sheets/1'>β-sheet</scene>, which provides an effective ligand-binding site, whereas the convex surface consists of <scene name='82/829346/Alpha_helix/1'>α-helices</scene>, which affect the curvature of the LRR domain.
-The N-terminal signal peptide is long of 33 amino. The extracellular domain contains 399 amino acids organized in 2 cysteine-rich domains (LRRNT and LRRCT) and 10 leucine rich domains (LRR). Each LRR domain is composed of 21 amino acids containing the conserved 11-aa sequence, LxxLxLxxN/ CxL, where x is any amino acid, and leucines and asparagine can be replaced with other hydrophobic residues. The leucine rich repeat domain forms a convex structure stabilized by a Phe spine. The concave surface is composed of a continuous β-sheet, which provides an effective ligand-binding site, whereas the convex surface consists of α-helices, which affect the curvature of the LRR domain.
 The N-terminal domain allows for the fixation of Nrxns which binds to the concave surface of the LRR1-LRR5 part of the protein. This fixation is mediated by calcium ions which interacts with the Asp144 and Asp212 of LRRTMT2. It was also observed that LRRTM2 Glu348 interacts with Ca2+ through a water molecule. In top of the Ca2+ mediated interaction, there is the formation of a hydrogen bound between the Asp352 of LRRTM2 and the Arg206 of Nrxns as well as hydrophobic interactions between the LRRTM2 Phe357 and Nrxns Leu208.
 The fixation of Nrxns doesn’t change the conformation of the protein aside from Glu348 flipping toward the calcium ions.
@@ Line 20: / Line 18: @@
 )	C-term fixation domain
 The cytoplasmic domain contains 73 amino acids. It has been shown that the deletion of 55 residues from the C-terminal domain leads to abnormal intracellular trafficking pathway. This results in LRRTM2 being present in everywhere in the cell. This domain also contains a PSD consensus cytoplasmic binding domain (ECEV) which binds PSD-95 (postsynaptic scaffolding protein)
 This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.