5dn2: Difference between revisions

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<StructureSection load='5dn2' size='340' side='right'caption='[[5dn2]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='5dn2' size='340' side='right'caption='[[5dn2]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5dn2]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DN2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DN2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5dn2]] is a 7 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=5DN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DN2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <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]] 1.95&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NRP2, VEGF165R2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), VEGFA, VEGF ([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=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <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'>[http://proteopedia.org/fgij/fg.htm?mol=5dn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dn2 OCA], [http://pdbe.org/5dn2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dn2 RCSB], [http://www.ebi.ac.uk/pdbsum/5dn2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dn2 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=5dn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dn2 OCA], [https://pdbe.org/5dn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dn2 RCSB], [https://www.ebi.ac.uk/pdbsum/5dn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dn2 ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/VEGFA_HUMAN VEGFA_HUMAN]] Defects in VEGFA are a cause of susceptibility to microvascular complications of diabetes type 1 (MVCD1) [MIM:[http://omim.org/entry/603933 603933]]. These are pathological conditions that develop in numerous tissues and organs as a consequence of diabetes mellitus. They include diabetic retinopathy, diabetic nephropathy leading to end-stage renal disease, and diabetic neuropathy. Diabetic retinopathy remains the major cause of new-onset blindness among diabetic adults. It is characterized by vascular permeability and increased tissue ischemia and angiogenesis.
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/NRP2_HUMAN NRP2_HUMAN]] High affinity receptor for semaphorins 3C, 3F, VEGF-165 and VEGF-145 isoforms of VEGF, and the PLGF-2 isoform of PGF. [[http://www.uniprot.org/uniprot/VEGFA_HUMAN VEGFA_HUMAN]] Growth factor active in angiogenesis, vasculogenesis and endothelial cell growth. Induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis and induces permeabilization of blood vessels. Binds to the FLT1/VEGFR1 and KDR/VEGFR2 receptors, heparan sulfate and heparin. NRP1/Neuropilin-1 binds isoforms VEGF-165 and VEGF-145. Isoform VEGF165B binds to KDR but does not activate downstream signaling pathways, does not activate angiogenesis and inhibits tumor growth.<ref>PMID:11427521</ref> <ref>PMID:15520188</ref> <ref>PMID:16489009</ref> 
[https://www.uniprot.org/uniprot/NRP2_HUMAN NRP2_HUMAN] High affinity receptor for semaphorins 3C, 3F, VEGF-165 and VEGF-145 isoforms of VEGF, and the PLGF-2 isoform of PGF.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Djordjevic, S]]
[[Category: Djordjevic S]]
[[Category: Fotinou, C]]
[[Category: Fotinou C]]
[[Category: Frankel, P]]
[[Category: Frankel P]]
[[Category: Rana, R]]
[[Category: Rana R]]
[[Category: Tsai, Y C.I]]
[[Category: Tsai YCI]]
[[Category: Zachary, I]]
[[Category: Zachary I]]
[[Category: Angiogenesis]]
[[Category: Heparin]]
[[Category: Neuropilin-2]]
[[Category: Receptor]]
[[Category: Signaling protein]]
[[Category: Vegfa]]

Latest revision as of 00:50, 29 June 2023

Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-AHuman NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A

Structural highlights

5dn2 is a 7 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 1.95Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NRP2_HUMAN High affinity receptor for semaphorins 3C, 3F, VEGF-165 and VEGF-145 isoforms of VEGF, and the PLGF-2 isoform of PGF.

Publication Abstract from PubMed

Neuropilin-2 is a transmembrane receptor involved in lymphangiogenesis and neuronal development. In adults, neuropilin-2 and its homologous protein neuropilin-1 have been implicated in cancers and infection. Molecular determinants of the ligand selectivity of neuropilins are poorly understood. We have identified and structurally characterized a zinc ion binding site on human neuropilin-2. The neuropilin-2-specific zinc ion binding site is located near the interface between domains b1 and b2 in the ectopic region of the protein, remote from the neuropilin binding site for its physiological ligand, i.e. vascular endothelial growth factor. We also present an X-ray crystal structure of the neuropilin-2 b1 domain in a complex with the C-terminal sub-domain of VEGF-A. Zn(2+) binding to neuropilin-2 destabilizes the protein structure but this effect was counteracted by heparin, suggesting that modifications by glycans and zinc in the extracellular matrix may affect functional neuropilin-2 ligand binding and signalling activity.

Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket.,Tsai YC, Fotinou C, Rana R, Yelland T, Frankel P, Zachary I, Djordjevic S FEBS J. 2016 May;283(10):1921-34. doi: 10.1111/febs.13711. Epub 2016 Apr 1. PMID:26991001[1]

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

See Also

References

  1. ↑ Tsai YC, Fotinou C, Rana R, Yelland T, Frankel P, Zachary I, Djordjevic S. Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket. FEBS J. 2016 May;283(10):1921-34. doi: 10.1111/febs.13711. Epub 2016 Apr 1. PMID:26991001 doi:http://dx.doi.org/10.1111/febs.13711

5dn2, resolution 1.95Å

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