6kok

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of SNX11/SNX10-PXe Chimera

Structural highlights

6kok is a 2 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 2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

SNX10_HUMAN Autosomal recessive malignant osteopetrosis. The disease is caused by mutations affecting the gene represented in this entry.^[1] ^[2] ^[3]

Function

SNX11_HUMAN May be involved in several stages of intracellular trafficking (By similarity).SNX10_HUMAN Probable phosphoinositide-binding protein involved in protein sorting and membrane trafficking in endosomes. Plays a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium. Required for the localization to the cilium of V-ATPase subunit ATP6V1D and ATP6V0D1, and RAB8A. Involved in osteoclast differentiation and therefore bone resorption.^[4] ^[5] ^[6]

Publication Abstract from PubMed

Phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) is an essential phosphoinositide required for endosome homeostasis and sorting for lysosomal degradation; however, the underlying mechanisms, especially in mammals, remain elusive or unexplored. Here we determined a structure of PI(3,5)P2 bound to Sorting Nexin 11 (SNX11) with an opened PPII-C loop. We also obtained an SNX11 structure with its PPII-C in "closed" form that serves as a potential PI3P-binding model. In addition, our results reveal that SNX11 can interact with the V1D subunit of vacuolar H(+)-ATPase (V-ATPase), which provides a link between PI(3,5)P2 and human V-ATPase and further evidence for their roles in the endosome homeostasis regulation. Lastly, a new apo-form structure of SNX11, combined with molecular dynamics (MD) studies, indicates that the alpha5 helix can unfold from the PX domain of SNX11 when targeting the membrane or interacting with its partner. Taken together, these findings identify a novel PI(3,5)P2 effector, which will shed light on the PIs recognizing mechanism and the understanding of the downstream sorting events triggered by different PI binding.

Molecular Basis for PI(3,5)P2 Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation.,Xu T, Gan Q, Wu B, Yin M, Xu J, Shu X, Liu J J Mol Biol. 2020 Jun 16. pii: S0022-2836(20)30406-X. doi:, 10.1016/j.jmb.2020.06.010. PMID:32561432^[7]

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

References

↑ Aker M, Rouvinski A, Hashavia S, Ta-Shma A, Shaag A, Zenvirt S, Israel S, Weintraub M, Taraboulos A, Bar-Shavit Z, Elpeleg O. An SNX10 mutation causes malignant osteopetrosis of infancy. J Med Genet. 2012 Apr;49(4):221-6. doi: 10.1136/jmedgenet-2011-100520. PMID:22499339 doi:http://dx.doi.org/10.1136/jmedgenet-2011-100520
↑ Megarbane A, Pangrazio A, Villa A, Chouery E, Maarawi J, Sabbagh S, Lefranc G, Sobacchi C. Homozygous stop mutation in the SNX10 gene in a consanguineous Iraqi boy with osteopetrosis and corpus callosum hypoplasia. Eur J Med Genet. 2013 Jan;56(1):32-5. doi: 10.1016/j.ejmg.2012.10.010. Epub 2012 , Oct 31. PMID:23123320 doi:http://dx.doi.org/10.1016/j.ejmg.2012.10.010
↑ Pangrazio A, Fasth A, Sbardellati A, Orchard PJ, Kasow KA, Raza J, Albayrak C, Albayrak D, Vanakker OM, De Moerloose B, Vellodi A, Notarangelo LD, Schlack C, Strauss G, Kuhl JS, Caldana E, Lo Iacono N, Susani L, Kornak U, Schulz A, Vezzoni P, Villa A, Sobacchi C. SNX10 mutations define a subgroup of human autosomal recessive osteopetrosis with variable clinical severity. J Bone Miner Res. 2013 May;28(5):1041-9. doi: 10.1002/jbmr.1849. PMID:23280965 doi:http://dx.doi.org/10.1002/jbmr.1849
↑ Qin B, He M, Chen X, Pei D. Sorting nexin 10 induces giant vacuoles in mammalian cells. J Biol Chem. 2006 Dec 1;281(48):36891-6. Epub 2006 Sep 29. PMID:17012226 doi:http://dx.doi.org/10.1074/jbc.M608884200
↑ Chen Y, Wu B, Xu L, Li H, Xia J, Yin W, Li Z, Shi D, Li S, Lin S, Shu X, Pei D. A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and in vivo. Cell Res. 2012 Feb;22(2):333-45. doi: 10.1038/cr.2011.134. Epub 2011 Aug 16. PMID:21844891 doi:http://dx.doi.org/10.1038/cr.2011.134
↑ Aker M, Rouvinski A, Hashavia S, Ta-Shma A, Shaag A, Zenvirt S, Israel S, Weintraub M, Taraboulos A, Bar-Shavit Z, Elpeleg O. An SNX10 mutation causes malignant osteopetrosis of infancy. J Med Genet. 2012 Apr;49(4):221-6. doi: 10.1136/jmedgenet-2011-100520. PMID:22499339 doi:http://dx.doi.org/10.1136/jmedgenet-2011-100520
↑ Xu T, Gan Q, Wu B, Yin M, Xu J, Shu X, Liu J. Molecular Basis for PI(3,5)P2 Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation. J Mol Biol. 2020 Jun 16. pii: S0022-2836(20)30406-X. doi:, 10.1016/j.jmb.2020.06.010. PMID:32561432 doi:http://dx.doi.org/10.1016/j.jmb.2020.06.010

1 Structural highlights
2 Disease
3 Function
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/6kok"

Categories: Homo sapiens | Large Structures | Liu J | Xu T

@@ Line 3: / Line 3: @@
 <StructureSection load='6kok' size='340' side='right'caption='[[6kok]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6kok]] is a 2 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=6KOK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KOK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6kok]] is a 2 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=6KOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KOK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6koi|6koi]], [[6koj|6koj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNX10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6kok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kok OCA], [https://pdbe.org/6kok PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kok RCSB], [https://www.ebi.ac.uk/pdbsum/6kok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kok 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=6kok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kok OCA], [http://pdbe.org/6kok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kok RCSB], [http://www.ebi.ac.uk/pdbsum/6kok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kok ProSAT]</span></td></tr>
 </table>
+== Disease ==
+[https://www.uniprot.org/uniprot/SNX10_HUMAN SNX10_HUMAN] Autosomal recessive malignant osteopetrosis. The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:22499339</ref> <ref>PMID:23123320</ref> <ref>PMID:23280965</ref>
 == Function ==
-[[http://www.uniprot.org/uniprot/SNX11_HUMAN SNX11_HUMAN]] May be involved in several stages of intracellular trafficking (By similarity).
+[https://www.uniprot.org/uniprot/SNX11_HUMAN SNX11_HUMAN] May be involved in several stages of intracellular trafficking (By similarity).[https://www.uniprot.org/uniprot/SNX10_HUMAN SNX10_HUMAN] Probable phosphoinositide-binding protein involved in protein sorting and membrane trafficking in endosomes. Plays a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium. Required for the localization to the cilium of V-ATPase subunit ATP6V1D and ATP6V0D1, and RAB8A. Involved in osteoclast differentiation and therefore bone resorption.<ref>PMID:17012226</ref> <ref>PMID:21844891</ref> <ref>PMID:22499339</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 21: @@
 </div>
 <div class="pdbe-citations 6kok" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Sorting nexin 3D structures|Sorting nexin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Liu, J]]
+[[Category: Liu J]]
-[[Category: Xu, T]]
+[[Category: Xu T]]
-[[Category: Phox-homology domain]]
-[[Category: Protein transport]]
-[[Category: Sorting nexin]]

6kok

From Proteopedia

Current revision

Crystal Structure of SNX11/SNX10-PXe Chimera

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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