2aki: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2aki.gif|left|200px]]


{{Structure
==Normal mode-based flexible fitted coordinates of a translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli==
|PDB= 2aki |SIZE=350|CAPTION= <scene name='initialview01'>2aki</scene>
<SX load='2aki' size='340' side='right' viewer='molstar' caption='[[2aki]], [[Resolution|resolution]] 14.90&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[2aki]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AKI FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 14.9&#8491;</td></tr>
|GENE= secG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), secY, prlA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), secE, prlG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2aki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aki OCA], [https://pdbe.org/2aki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aki RCSB], [https://www.ebi.ac.uk/pdbsum/2aki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aki ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=[[2akh|2AKH]]
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2aki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aki OCA], [http://www.ebi.ac.uk/pdbsum/2aki PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2aki RCSB]</span>
[https://www.uniprot.org/uniprot/SECY_ECOLI SECY_ECOLI] 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. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.[HAMAP-Rule:MF_01465]
}}
== 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/ak/2aki_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/main_output.php?pdb_ID=2aki ConSurf].
<div style="clear:both"></div>


'''Normal mode-based flexible fitted coordinates of a translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli'''
==See Also==
 
*[[Preprotein translocase 3D structures|Preprotein translocase 3D structures]]
 
__TOC__
==Overview==
</SX>
Secreted and membrane proteins are translocated across or into cell membranes through a protein-conducting channel (PCC). Here we present a cryo-electron microscopy reconstruction of the Escherichia coli PCC, SecYEG, complexed with the ribosome and a nascent chain containing a signal anchor. This reconstruction shows a messenger RNA, three transfer RNAs, the nascent chain, and detailed features of both a translocating PCC and a second, non-translocating PCC bound to mRNA hairpins. The translocating PCC forms connections with ribosomal RNA hairpins on two sides and ribosomal proteins at the back, leaving a frontal opening. Normal mode-based flexible fitting of the archaeal SecYEbeta structure into the PCC electron microscopy densities favours a front-to-front arrangement of two SecYEG complexes in the PCC, and supports channel formation by the opening of two linked SecY halves during polypeptide translocation. On the basis of our observation in the translocating PCC of two segregated pores with different degrees of access to bulk lipid, we propose a model for co-translational protein translocation.
 
==About this Structure==
2AKI is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKI OCA].
 
==Reference==
Structure of the E. coli protein-conducting channel bound to a translating ribosome., Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL 3rd, Ban N, Frank J, Nature. 2005 Nov 17;438(7066):318-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16292303 16292303]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Ban, N.]]
[[Category: Ban N]]
[[Category: Frank, J.]]
[[Category: Brooks III CL]]
[[Category: III, C L.Brooks.]]
[[Category: Frank J]]
[[Category: Jenni, S.]]
[[Category: Jenni S]]
[[Category: Mitra, K.]]
[[Category: Mitra K]]
[[Category: Schaffitzel, C.]]
[[Category: Schaffitzel C]]
[[Category: Shaikh, T.]]
[[Category: Shaikh T]]
[[Category: Tama, F.]]
[[Category: Tama F]]
[[Category: protein transport]]
[[Category: translocation]]
[[Category: transmembrane]]
[[Category: transport]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:54:02 2008''

Latest revision as of 12:13, 14 February 2024

Normal mode-based flexible fitted coordinates of a translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coliNormal mode-based flexible fitted coordinates of a translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli

2aki, resolution 14.90Å

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2aki&oldid=4057750"