2om7: Difference between revisions

Latest revision as of 00:20, 28 December 2023

Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors

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Structural highlights

2om7 is a 10 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 7.3Å
Ligands:	4SU, 5MC, 5MU, H2U, PSU
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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

Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S*EF-G ribosomal complex at 7.3 A resolution and the crystal structure of EF-G-2*GTP, an EF-G homolog, at 2.2 A resolution are presented. EF-G-2*GTP is structurally distinct from previous EF-G structures, and in the context of the cryo-EM structure, the conformational changes are associated with ribosome binding and activation of the GTP binding pocket. The P loop and switch II approach A2660-A2662 in helix 95 of the 23S rRNA, indicating an important role for these conserved bases. Furthermore, the ordering of the functionally important switch I and II regions, which interact with the bound GTP, is dependent on interactions with the ribosome in the ratcheted conformation. Therefore, a network of interaction with the ribosome establishes the active GTP conformation of EF-G and thus facilitates GTP hydrolysis and tRNA translocation.

Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.,Connell SR, Takemoto C, Wilson DN, Wang H, Murayama K, Terada T, Shirouzu M, Rost M, Schuler M, Giesebrecht J, Dabrowski M, Mielke T, Fucini P, Yokoyama S, Spahn CM Mol Cell. 2007 Mar 9;25(5):751-64. PMID:17349960^[1]

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

References

↑ Connell SR, Takemoto C, Wilson DN, Wang H, Murayama K, Terada T, Shirouzu M, Rost M, Schuler M, Giesebrecht J, Dabrowski M, Mielke T, Fucini P, Yokoyama S, Spahn CM. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol Cell. 2007 Mar 9;25(5):751-64. PMID:17349960 doi:10.1016/j.molcel.2007.01.027

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Connell SR, Takemoto C, Wilson DN, Wang H, Murayama K, Terada T, Shirouzu M, Rost M, Schuler M, Giesebrecht J, Dabrowski M, Mielke T, Fucini P, Yokoyama S, Spahn CM. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol Cell. 2007 Mar 9;25(5):751-64. PMID:17349960 doi:10.1016/j.molcel.2007.01.027

[1]

@@ Line 1: / Line 1: @@
 ==Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors==
-<StructureSection load='2om7' size='340' side='right' caption='[[2om7]], [[Resolution|resolution]] 7.30&Aring;' scene=''>
+<SX load='2om7' size='340' side='right' viewer='molstar' caption='[[2om7]], [[Resolution|resolution]] 7.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2om7]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OM7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OM7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2om7]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OM7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OM7 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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]] 7.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2j00|2j00]], [[2j01|2j01]], [[1yl3|1yl3]], [[1yl4|1yl4]], [[1wdt|1wdt]], [[1fnm|1fnm]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fusA, fus ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=2om7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2om7 OCA], [https://pdbe.org/2om7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2om7 RCSB], [https://www.ebi.ac.uk/pdbsum/2om7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2om7 ProSAT], [https://www.topsan.org/Proteins/RSGI/2om7 TOPSAN]</span></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=2om7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2om7 OCA], [http://pdbe.org/2om7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2om7 RCSB], [http://www.ebi.ac.uk/pdbsum/2om7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2om7 ProSAT], [http://www.topsan.org/Proteins/RSGI/2om7 TOPSAN]</span></td></tr>
 </table>
-== Function ==
-[[http://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B]  Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RL1_THET8 RL1_THET8]] Directly binds to 23S rRNA. Forms what is known as the L1 stalk, which protrudes beyond the 70S ribosome surface. The stalk is preferentially stabilized in 70S versus 50S crystals. Interacts with the E site tRNA, blocking the exit path. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_01318_B]  Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318_B] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [[http://www.uniprot.org/uniprot/EFG_THETH EFG_THETH]] Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.
 == 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/om/2om7_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/om/2om7_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 29: @@
 ==See Also==
+*[[Elongation factor 3D structures|Elongation factor 3D structures]]
+*[[Ribosomal protein L1|Ribosomal protein L1]]
 *[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[TRNA|TRNA]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Connell, S R]]
+[[Category: Connell SR]]
-[[Category: Dabrowski, M]]
+[[Category: Dabrowski M]]
-[[Category: Fucini, P]]
+[[Category: Fucini P]]
-[[Category: Giesebrecht, J]]
+[[Category: Giesebrecht J]]
-[[Category: Mielke, T]]
+[[Category: Mielke T]]
-[[Category: Rost, M]]
+[[Category: Rost M]]
-[[Category: Schueler, M]]
+[[Category: Schueler M]]
-[[Category: Spahn, C M.T]]
+[[Category: Spahn CMT]]
-[[Category: Wilson, D N]]
+[[Category: Wilson DN]]
-[[Category: Ribosome]]
-[[Category: Rna-protein complex]]

2om7: Difference between revisions

Latest revision as of 00:20, 28 December 2023

Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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