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.

2re9

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of TL1A at 2.1 A

Structural highlights

2re9 is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TNF15_HUMAN Receptor for TNFRSF25 and TNFRSF6B. Mediates activation of NF-kappa-B. Inhibits vascular endothelial growth and angiogenesis (in vitro). Promotes activation of caspases and apoptosis.^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

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

Publication Abstract from PubMed

The TNF family has been one of the most intensively studied protein families in the past two decades and it has rapidly expanded through the era of genomics and bioinformatics. However, the structural basis of the functional and interactional similarities and differences of this family is poorly understood. TL1A is a recently identified TNF family member that has received increasing attention. Here, the crystal structure of human TL1A is reported. TL1A forms a homotrimer with each monomer assuming a jellyroll beta-sandwich fold. The CD loop in TL1A is the longest among the TNF ligand members with known structure and the AA' loop in TL1A is the second longest after that in TRAIL, where part of it is disordered. Both these loops are known to participate in receptor binding in TNFbeta/LTalpha. The AA' loop may be very different in other TL1A variants if the overall fold is to be preserved.

X-ray crystal structure of TNF ligand family member TL1A at 2.1A.,Jin T, Guo F, Kim S, Howard A, Zhang YZ Biochem Biophys Res Commun. 2007 Dec 7;364(1):1-6. Epub 2007 Oct 1. PMID:17935696^[5]

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

References

↑ Zhai Y, Ni J, Jiang GW, Lu J, Xing L, Lincoln C, Carter KC, Janat F, Kozak D, Xu S, Rojas L, Aggarwal BB, Ruben S, Li LY, Gentz R, Yu GL. VEGI, a novel cytokine of the tumor necrosis factor family, is an angiogenesis inhibitor that suppresses the growth of colon carcinomas in vivo. FASEB J. 1999 Jan;13(1):181-9. PMID:9872942
↑ Chew LJ, Pan H, Yu J, Tian S, Huang WQ, Zhang JY, Pang S, Li LY. A novel secreted splice variant of vascular endothelial cell growth inhibitor. FASEB J. 2002 May;16(7):742-4. Epub 2002 Mar 26. PMID:11923219 doi:10.1096/fj.01-0757fje
↑ Migone TS, Zhang J, Luo X, Zhuang L, Chen C, Hu B, Hong JS, Perry JW, Chen SF, Zhou JX, Cho YH, Ullrich S, Kanakaraj P, Carrell J, Boyd E, Olsen HS, Hu G, Pukac L, Liu D, Ni J, Kim S, Gentz R, Feng P, Moore PA, Ruben SM, Wei P. TL1A is a TNF-like ligand for DR3 and TR6/DcR3 and functions as a T cell costimulator. Immunity. 2002 Mar;16(3):479-92. PMID:11911831
↑ Haridas V, Shrivastava A, Su J, Yu GL, Ni J, Liu D, Chen SF, Ni Y, Ruben SM, Gentz R, Aggarwal BB. VEGI, a new member of the TNF family activates nuclear factor-kappa B and c-Jun N-terminal kinase and modulates cell growth. Oncogene. 1999 Nov 11;18(47):6496-504. PMID:10597252 doi:10.1038/sj.onc.1203059
↑ Jin T, Guo F, Kim S, Howard A, Zhang YZ. X-ray crystal structure of TNF ligand family member TL1A at 2.1A. Biochem Biophys Res Commun. 2007 Dec 7;364(1):1-6. Epub 2007 Oct 1. PMID:17935696 doi:http://dx.doi.org/10.1016/j.bbrc.2007.09.097

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2re9"

@@ Line 1: / Line 1: @@
 ==Crystal structure of TL1A at 2.1 A==
-<StructureSection load='2re9' size='340' side='right' caption='[[2re9]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2re9' size='340' side='right'caption='[[2re9]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2re9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RE9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2re9]] is a 3 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=2RE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RE9 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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]] 2.1&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TNFSF15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2re9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2re9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2re9 RCSB], [http://www.ebi.ac.uk/pdbsum/2re9 PDBsum]</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=2re9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2re9 OCA], [https://pdbe.org/2re9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2re9 RCSB], [https://www.ebi.ac.uk/pdbsum/2re9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2re9 ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TNF15_HUMAN TNF15_HUMAN] Receptor for TNFRSF25 and TNFRSF6B. Mediates activation of NF-kappa-B. Inhibits vascular endothelial growth and angiogenesis (in vitro). Promotes activation of caspases and apoptosis.<ref>PMID:9872942</ref> <ref>PMID:11923219</ref> <ref>PMID:11911831</ref> <ref>PMID:10597252</ref>
 == 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/re/2re9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/2re9_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/chain_selection.php?pdb_ID=2ata 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=2re9 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2re9" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Tumor necrosis factor ligand superfamily 3D structures|Tumor necrosis factor ligand superfamily 3D structures]]
 == References ==
 <references/>
@@ Line 30: / Line 37: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Guo, F.]]
+[[Category: Large Structures]]
-[[Category: Howard, A J.]]
+[[Category: Guo F]]
-[[Category: Jin, T C.]]
+[[Category: Howard AJ]]
-[[Category: Kim, S.]]
+[[Category: Jin TC]]
-[[Category: Zhang, Y Z.]]
+[[Category: Kim S]]
-[[Category: Cytokine]]
+[[Category: Zhang YZ]]
-[[Category: Homotrimer]]
-[[Category: Hormone-growth factor complex]]
-[[Category: Membrane]]
-[[Category: Metal binding]]
-[[Category: Transmembrane]]
-[[Category: Vegi]]

2re9

From Proteopedia

Current revision

Crystal structure of TL1A at 2.1 A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox