3dmd: Difference between revisions

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-{{Seed}}
-[[Image:3dmd.jpg|left|200px]]
-<!--
+==Structures and Conformations in Solution of the Signal Recognition Particle Receptor from the archaeon Pyrococcus furiosus==
-The line below this paragraph, containing "STRUCTURE_3dmd", creates the "Structure Box" on the page.
+<StructureSection load='3dmd' size='340' side='right'caption='[[3dmd]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3dmd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DMD FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.21&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3dmd|  PDB=3dmd  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmd OCA], [https://pdbe.org/3dmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dmd RCSB], [https://www.ebi.ac.uk/pdbsum/3dmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dmd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8U051_PYRFU Q8U051_PYRFU] Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC) (By similarity).[HAMAP-Rule:MF_00920]
+== 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/dm/3dmd_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=3dmd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In all organisms, a ribonucleoprotein called the signal recognition particle (SRP) and its receptor (SR) target nascent proteins from the ribosome to the translocon for secretion or membrane insertion. We present the first X-ray structures of an archeal FtsY, the receptor from the hyper-thermophile Pyrococcus furiosus (Pfu), in its free and GDP*magnesium-bound forms. The highly charged N-terminal domain of Pfu-FtsY is distinguished by a long N-terminal helix. The basic charges on the surface of this helix are likely to regulate interactions at the membrane. A peripheral GDP bound near a regulatory motif could indicate a site of interaction between the receptor and ribosomal or SRP RNAs. Small angle X-ray scattering and analytical ultracentrifugation indicate that the crystal structure of Pfu-FtsY correlates well with the average conformation in solution. Based on previous structures of two sub-complexes, we propose a model of the core of archeal and eukaryotic SRP*SR targeting complexes.
-===Structures and Conformations in Solution of the Signal Recognition Particle Receptor from the archaeon Pyrococcus furiosus===
+Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane.,Egea PF, Tsuruta H, de Leon GP, Napetschnig J, Walter P, Stroud RM PLoS ONE. 2008;3(11):e3619. Epub 2008 Nov 3. PMID:18978942<ref>PMID:18978942</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dmd" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18978942}}, adds the Publication Abstract to the page
+*[[Signal recognition particle receptor|Signal recognition particle receptor]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18978942 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18978942}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DMD is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DMD OCA].
-==Reference==
-Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane., Egea PF, Tsuruta H, de Leon GP, Napetschnig J, Walter P, Stroud RM, PLoS ONE. 2008;3(11):e3619. Epub 2008 Nov 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18978942 18978942]
 [[Category: Pyrococcus furiosus]]
-[[Category: Egea, P F.]]
+[[Category: Egea PF]]
-[[Category: Napetschnig, J.]]
+[[Category: Napetschnig J]]
-[[Category: Stroud, R M.]]
+[[Category: Stroud RM]]
-[[Category: Tsuruta, H.]]
+[[Category: Tsuruta H]]
-[[Category: Walter, P.]]
+[[Category: Walter P]]
-[[Category: Ftsy]]
-[[Category: Protein-targeting]]
-[[Category: Signal recognition particle receptor]]
-[[Category: Srp-gtpase]]
-[[Category: Transport protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 12 10:47:38 2008''