2k4t

From Proteopedia

(Difference between revisions)

Current revision

Solution structure of human VDAC-1 in LDAO micelles

Structural highlights

2k4t is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded beta barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a beltlike fashion. In the presence of cholesterol, recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to those of the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-x(L), for reduced beta-nicotinamide adenine dinucleotide, and for cholesterol. Bcl-x(L) interacts with the VDAC barrel laterally at strands 17 and 18.

Solution structure of the integral human membrane protein VDAC-1 in detergent micelles.,Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, Wagner G Science. 2008 Aug 29;321(5893):1206-10. PMID:18755977^[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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
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/2k4t"

@@ Line 1: / Line 1: @@
 ==Solution structure of human VDAC-1 in LDAO micelles==
-<StructureSection load='2k4t' size='340' side='right' caption='[[2k4t]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2k4t' size='340' side='right'caption='[[2k4t]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2k4t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K4T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2k4t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K4T FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VDAC1, VDAC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2k4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k4t OCA], [http://pdbe.org/2k4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k4t RCSB], [http://www.ebi.ac.uk/pdbsum/2k4t PDBsum]</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=2k4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k4t OCA], [https://pdbe.org/2k4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k4t RCSB], [https://www.ebi.ac.uk/pdbsum/2k4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k4t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k4/2k4t_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k4/2k4t_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2k4t ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 30: @@
 ==See Also==
-*[[Ion channels|Ion channels]]
+*[[Ion channels 3D structures|Ion channels 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Colombini, M]]
+[[Category: Large Structures]]
-[[Category: Garces, R G]]
+[[Category: Colombini M]]
-[[Category: Hiller, S]]
+[[Category: Garces RG]]
-[[Category: Malia, T J]]
+[[Category: Hiller S]]
-[[Category: Orekhov, V Y]]
+[[Category: Malia TJ]]
-[[Category: Wagner, G]]
+[[Category: Orekhov VY]]
-[[Category: Apoptosis]]
+[[Category: Wagner G]]
-[[Category: Host-virus interaction]]
-[[Category: Ion transport]]
-[[Category: Membrane]]
-[[Category: Membrane protein]]
-[[Category: Mitochondrion]]
-[[Category: Outer membrane]]
-[[Category: Phosphoprotein]]
-[[Category: Porin]]
-[[Category: Transmembrane]]
-[[Category: Transport protein]]

2k4t

From Proteopedia

Current revision

Solution structure of human VDAC-1 in LDAO micelles

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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