5xdn: Difference between revisions

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-'''Unreleased structure'''
-The entry 5xdn is ON HOLD
+==Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group==
+<StructureSection load='5xdn' size='340' side='right'caption='[[5xdn]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5xdn]] 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=5XDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XDN FirstGlance]. <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]] 3.15&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</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=5xdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdn OCA], [https://pdbe.org/5xdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xdn RCSB], [https://www.ebi.ac.uk/pdbsum/5xdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VDAC1_HUMAN VDAC1_HUMAN] Forms a channel through the mitochondrial outer membrane and also the plasma membrane. The channel at the outer mitochondrial membrane allows diffusion of small hydrophilic molecules; in the plasma membrane it is involved in cell volume regulation and apoptosis. It adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis.<ref>PMID:11845315</ref> <ref>PMID:15033708</ref> <ref>PMID:18755977</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad-range screening using a bicelle crystallization method produced crystals in space groups C222 and P221 21 , which diffracted to a resolution of 3.10 and 3.15 A, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P221 21 were oriented anti-parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with beta-strands, hydrophilic interactions with loop regions, and protein-lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo- or hetero-oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis-regulating proteins in the Bcl-2 family.
-Authors:
+Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1.,Hosaka T, Okazaki M, Kimura-Someya T, Ishizuka-Katsura Y, Ito K, Yokoyama S, Dodo K, Sodeoka M, Shirouzu M Protein Sci. 2017 Sep;26(9):1749-1758. doi: 10.1002/pro.3211. Epub 2017 Jun 21. PMID:28608415<ref>PMID:28608415</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5xdn" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ion channels 3D structures|Ion channels 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Hosaka T]]
+[[Category: Kimura-Someya T]]
+[[Category: Shirouzu M]]