9jyx: Difference between revisions

Latest revision as of 07:10, 15 October 2025

Crystal structure of Nir2 DDHD domain

Structural highlights

9jyx 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 2.798Å
Ligands:	PO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PITM1_HUMAN Catalyzes the transfer of phosphatidylinositol (PI) between membranes (PubMed:10531358, PubMed:22822086). Binds PI, phosphatidylcholine (PC) and phosphatidic acid (PA) with the binding affinity order of PI > PA > PC (PubMed:22822086). Regulates RHOA activity, and plays a role in cytoskeleton remodeling (PubMed:11909959). Necessary for normal completion of cytokinesis (PubMed:15125835). Plays a role in maintaining normal diacylglycerol levels in the Golgi apparatus (PubMed:15723057). Necessary for maintaining the normal structure of the endoplasmic reticulum and the Golgi apparatus (PubMed:15545272). Required for protein export from the endoplasmic reticulum and the Golgi (PubMed:15723057). Binds calcium ions (PubMed:10022914).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

References

↑ Lev S, Hernandez J, Martinez R, Chen A, Plowman G, Schlessinger J. Identification of a novel family of targets of PYK2 related to Drosophila retinal degeneration B (rdgB) protein. Mol Cell Biol. 1999 Mar;19(3):2278-88. PMID:10022914 doi:10.1128/MCB.19.3.2278
↑ Fullwood Y, dos Santos M, Hsuan JJ. Cloning and characterization of a novel human phosphatidylinositol transfer protein, rdgBbeta. J Biol Chem. 1999 Oct 29;274(44):31553-8. PMID:10531358 doi:10.1074/jbc.274.44.31553
↑ Tian D, Litvak V, Toledo-Rodriguez M, Carmon S, Lev S. Nir2, a novel regulator of cell morphogenesis. Mol Cell Biol. 2002 Apr;22(8):2650-62. PMID:11909959 doi:10.1128/MCB.22.8.2650-2662.2002
↑ Amarilio R, Ramachandran S, Sabanay H, Lev S. Differential regulation of endoplasmic reticulum structure through VAP-Nir protein interaction. J Biol Chem. 2005 Feb 18;280(7):5934-44. PMID:15545272 doi:10.1074/jbc.M409566200
↑ Litvak V, Dahan N, Ramachandran S, Sabanay H, Lev S. Maintenance of the diacylglycerol level in the Golgi apparatus by the Nir2 protein is critical for Golgi secretory function. Nat Cell Biol. 2005 Mar;7(3):225-34. PMID:15723057 doi:10.1038/ncb1221
↑ Garner K, Hunt AN, Koster G, Somerharju P, Groves E, Li M, Raghu P, Holic R, Cockcroft S. Phosphatidylinositol transfer protein, cytoplasmic 1 (PITPNC1) binds and transfers phosphatidic acid. J Biol Chem. 2012 Sep 14;287(38):32263-76. PMID:22822086 doi:10.1074/jbc.M112.375840

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Lev S, Hernandez J, Martinez R, Chen A, Plowman G, Schlessinger J. Identification of a novel family of targets of PYK2 related to Drosophila retinal degeneration B (rdgB) protein. Mol Cell Biol. 1999 Mar;19(3):2278-88. PMID:10022914 doi:10.1128/MCB.19.3.2278

[2] Fullwood Y, dos Santos M, Hsuan JJ. Cloning and characterization of a novel human phosphatidylinositol transfer protein, rdgBbeta. J Biol Chem. 1999 Oct 29;274(44):31553-8. PMID:10531358 doi:10.1074/jbc.274.44.31553

[3] Tian D, Litvak V, Toledo-Rodriguez M, Carmon S, Lev S. Nir2, a novel regulator of cell morphogenesis. Mol Cell Biol. 2002 Apr;22(8):2650-62. PMID:11909959 doi:10.1128/MCB.22.8.2650-2662.2002

[4] Amarilio R, Ramachandran S, Sabanay H, Lev S. Differential regulation of endoplasmic reticulum structure through VAP-Nir protein interaction. J Biol Chem. 2005 Feb 18;280(7):5934-44. PMID:15545272 doi:10.1074/jbc.M409566200

[5] Litvak V, Dahan N, Ramachandran S, Sabanay H, Lev S. Maintenance of the diacylglycerol level in the Golgi apparatus by the Nir2 protein is critical for Golgi secretory function. Nat Cell Biol. 2005 Mar;7(3):225-34. PMID:15723057 doi:10.1038/ncb1221

[6] Garner K, Hunt AN, Koster G, Somerharju P, Groves E, Li M, Raghu P, Holic R, Cockcroft S. Phosphatidylinositol transfer protein, cytoplasmic 1 (PITPNC1) binds and transfers phosphatidic acid. J Biol Chem. 2012 Sep 14;287(38):32263-76. PMID:22822086 doi:10.1074/jbc.M112.375840

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9jyx is ON HOLD  until 2027-03-31
+==Crystal structure of Nir2 DDHD domain==
+<StructureSection load='9jyx' size='340' side='right'caption='[[9jyx]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9jyx]] 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=9JYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9JYX FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.798&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=9jyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9jyx OCA], [https://pdbe.org/9jyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9jyx RCSB], [https://www.ebi.ac.uk/pdbsum/9jyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9jyx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PITM1_HUMAN PITM1_HUMAN] Catalyzes the transfer of phosphatidylinositol (PI) between membranes (PubMed:10531358, PubMed:22822086). Binds PI, phosphatidylcholine (PC) and phosphatidic acid (PA) with the binding affinity order of PI > PA > PC (PubMed:22822086). Regulates RHOA activity, and plays a role in cytoskeleton remodeling (PubMed:11909959). Necessary for normal completion of cytokinesis (PubMed:15125835). Plays a role in maintaining normal diacylglycerol levels in the Golgi apparatus (PubMed:15723057). Necessary for maintaining the normal structure of the endoplasmic reticulum and the Golgi apparatus (PubMed:15545272). Required for protein export from the endoplasmic reticulum and the Golgi (PubMed:15723057). Binds calcium ions (PubMed:10022914).<ref>PMID:10022914</ref> <ref>PMID:10531358</ref> <ref>PMID:11909959</ref> <ref>PMID:15545272</ref> <ref>PMID:15723057</ref> <ref>PMID:22822086</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Kim D]]
+[[Category: Lee C]]

9jyx: Difference between revisions

Latest revision as of 07:10, 15 October 2025

Crystal structure of Nir2 DDHD domain

Structural highlights

Function

References

Contents

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