5xdn

From Proteopedia

(Difference between revisions)

Revision as of 06:46, 14 October 2020

Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group

Structural highlights

5xdn is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	5xdo
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3]

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.

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^[4]

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

References

↑ Thinnes FP, Walter G, Hellmann KP, Hellmann T, Merker R, Kiafard Z, Eben-Brunnen J, Schwarzer C, Gotz H, Hilschmann N. Gadolinium as an opener of the outwardly rectifying Cl(-) channel (ORCC). Is there relevance for cystic fibrosis therapy? Pflugers Arch. 2001;443 Suppl 1:S111-6. Epub 2001 Jul 7. PMID:11845315 doi:http://dx.doi.org/10.1007/s004240100656
↑ Verrier F, Mignotte B, Jan G, Brenner C. Study of PTPC composition during apoptosis for identification of viral protein target. Ann N Y Acad Sci. 2003 Dec;1010:126-42. PMID:15033708
↑ Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, Wagner G. Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science. 2008 Aug 29;321(5893):1206-10. PMID:18755977 doi:321/5893/1206
↑ Hosaka T, Okazaki M, Kimura-Someya T, Ishizuka-Katsura Y, Ito K, Yokoyama S, Dodo K, Sodeoka M, Shirouzu M. Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1. Protein Sci. 2017 Sep;26(9):1749-1758. doi: 10.1002/pro.3211. Epub 2017 Jun 21. PMID:28608415 doi:http://dx.doi.org/10.1002/pro.3211

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5xdn"

@@ Line 1: / Line 1: @@
 ==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=''>
+<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. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XDN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xdn]] is a 2 chain structure. 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 [http://proteopedia.org/fgij/fg.htm?mol=5XDN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xdo|5xdo]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdn OCA], [http://pdbe.org/5xdn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xdn RCSB], [http://www.ebi.ac.uk/pdbsum/5xdn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdn 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=5xdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdn OCA], [http://pdbe.org/5xdn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xdn RCSB], [http://www.ebi.ac.uk/pdbsum/5xdn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdn ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5xdn" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ion channels 3D structures|Ion channels 3D structures]]
+*[[User:Kasha Maslowski/Biological Molecules Classification Lesson - High School Biology|User:Kasha Maslowski/Biological Molecules Classification Lesson - High School Biology]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Hosaka, T]]
 [[Category: Kimura-Someya, T]]

5xdn

From Proteopedia

Revision as of 06:46, 14 October 2020

Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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