3dkn: Difference between revisions

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==Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum==
==Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum==
<StructureSection load='3dkn' size='340' side='right' caption='[[3dkn]], [[Resolution|resolution]] 8.70&Aring;' scene=''>
<SX load='3dkn' size='340' side='right' viewer='molstar' caption='[[3dkn]], [[Resolution|resolution]] 8.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3dkn]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DKN FirstGlance]. <br>
<table><tr><td colspan='2'>[[3dkn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKN FirstGlance]. <br>
</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=3dkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dkn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dkn RCSB], [http://www.ebi.ac.uk/pdbsum/3dkn PDBsum]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 8.7&#8491;</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=3dkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dkn OCA], [https://pdbe.org/3dkn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dkn RCSB], [https://www.ebi.ac.uk/pdbsum/3dkn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dkn ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SECY_METJA SECY_METJA] The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/3dkn_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/3dkn_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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=3dkn ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we report the structure of a ribosome-channel complex from mammalian endoplasmic reticulum in which the channel has been visualized at 11 A resolution. In this complex, single copies of Sec61 and TRAP associate with a nontranslating ribosome and this stoichiometry was verified by quantitative mass spectrometry. A bilayer-like density surrounds the channel and can be attributed to lipid and detergent. The crystal structure of an archaeal homolog of the Sec61 complex was then docked into the map. In this model, two cytoplasmic loops of Sec61 may interact with RNA helices H6, H7, and H50, while the central pore is located below the ribosome tunnel exit. Hence, this copy of Sec61 is positioned to capture and translocate the nascent chain. Finally, we show that mammalian and bacterial ribosome-channel complexes have similar architectures.
Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome.,Menetret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, Akey CW Structure. 2008 Jul;16(7):1126-37. PMID:18611385<ref>PMID:18611385</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Preprotein translocase|Preprotein translocase]]
*[[Preprotein translocase 3D structures|Preprotein translocase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</SX>
[[Category: Canis lupus familiaris]]
[[Category: Canis lupus familiaris]]
[[Category: Akey, C]]
[[Category: Large Structures]]
[[Category: Menetret, J F]]
[[Category: Akey C]]
[[Category: Co-translational translocation]]
[[Category: Menetret J-F]]
[[Category: Endoplasmic reticulum]]
[[Category: Protein transport-rna complex]]
[[Category: Ribosome-channel complex]]

Latest revision as of 12:41, 21 February 2024

Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulumSec61 in the Canine ribosome-channel complex from the endoplasmic reticulum

3dkn, resolution 8.70Å

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