9xtc: Difference between revisions

Latest revision as of 06:34, 8 April 2026

E.coli delta lepA 30S ribosomal subunit class C, body domain

Structural highlights

9xtc is a 10 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.1Å
Ligands:	2MG, 4OC, D2T, G7M, MA6, MG, PSU, UR3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS6_ECOLI Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360]

Publication Abstract from PubMed

The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal subunit biogenesis. Here, using cryo-electron microscopy, we characterized 30S subunits isolated from an Escherichia coli strain with a deleted lepA gene. The cryo-EM maps for âlepA 30S particles were divided into classes corresponding to consecutive assembly intermediates: from particles characterized by unformed helices h44/h45 of the central decoding center (CDR) and highly flexible head, through intermediates with a distorted CDR and a partial stabilization of the head, to near-mature 30S subunits with correctly docked h44 in the CDR, accessible 3' end of 16S rRNA for translation but significant flexibility in head domain. Cryo-EM analysis of DeltalepA 30S intermediates revealed that they predominantly proceed to nearly mature functional state and exhibit suboptimal flexibility in the head domain. This finding suggests that LepA likely contributes to the final proper stabilization of the 3' domain of the 30S subunit during ribosome assembly.

The Conserved GTPase LepA May Contribute to the Final Proper Stabilization of the 3' Domain of the 30S Subunit During Ribosome Assembly.,Kravchenko O, Maksimova E, Baymukhametov T, Eliseeva I, Stolboushkina E Int J Mol Sci. 2026 Jan 3;27(1):489. doi: 10.3390/ijms27010489. PMID:41516366^[1]

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

References

↑ Kravchenko O, Maksimova E, Baymukhametov T, Eliseeva I, Stolboushkina E. The Conserved GTPase LepA May Contribute to the Final Proper Stabilization of the 3' Domain of the 30S Subunit During Ribosome Assembly. Int J Mol Sci. 2026 Jan 3;27(1):489. PMID:41516366 doi:10.3390/ijms27010489

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OCA

[1] Kravchenko O, Maksimova E, Baymukhametov T, Eliseeva I, Stolboushkina E. The Conserved GTPase LepA May Contribute to the Final Proper Stabilization of the 3' Domain of the 30S Subunit During Ribosome Assembly. Int J Mol Sci. 2026 Jan 3;27(1):489. PMID:41516366 doi:10.3390/ijms27010489

[1]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9xtc is ON HOLD  until Paper Publication
+==E.coli delta lepA 30S ribosomal subunit class C, body domain==
+<StructureSection load='9xtc' size='340' side='right'caption='[[9xtc]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9xtc]] is a 10 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=9XTC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9XTC FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=D2T:(3R)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>D2T</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></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=9xtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9xtc OCA], [https://pdbe.org/9xtc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9xtc RCSB], [https://www.ebi.ac.uk/pdbsum/9xtc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9xtc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS6_ECOLI RS6_ECOLI] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal subunit biogenesis. Here, using cryo-electron microscopy, we characterized 30S subunits isolated from an Escherichia coli strain with a deleted lepA gene. The cryo-EM maps for âlepA 30S particles were divided into classes corresponding to consecutive assembly intermediates: from particles characterized by unformed helices h44/h45 of the central decoding center (CDR) and highly flexible head, through intermediates with a distorted CDR and a partial stabilization of the head, to near-mature 30S subunits with correctly docked h44 in the CDR, accessible 3' end of 16S rRNA for translation but significant flexibility in head domain. Cryo-EM analysis of DeltalepA 30S intermediates revealed that they predominantly proceed to nearly mature functional state and exhibit suboptimal flexibility in the head domain. This finding suggests that LepA likely contributes to the final proper stabilization of the 3' domain of the 30S subunit during ribosome assembly.
-Authors: Kravchenko, O.V., Maksimova, E.M., Baymukhametov, T.N., Stolboushkina, E.A.
+The Conserved GTPase LepA May Contribute to the Final Proper Stabilization of the 3' Domain of the 30S Subunit During Ribosome Assembly.,Kravchenko O, Maksimova E, Baymukhametov T, Eliseeva I, Stolboushkina E Int J Mol Sci. 2026 Jan 3;27(1):489. doi: 10.3390/ijms27010489. PMID:41516366<ref>PMID:41516366</ref>
-Description: E.coli delta lepA 30S ribosomal subunit class C, body domain
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Kravchenko, O.V]]
+<div class="pdbe-citations 9xtc" style="background-color:#fffaf0;"></div>
-[[Category: Baymukhametov, T.N]]
+== References ==
-[[Category: Stolboushkina, E.A]]
+<references/>
-[[Category: Maksimova, E.M]]
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Baymukhametov TN]]
+[[Category: Kravchenko OV]]
+[[Category: Maksimova EM]]
+[[Category: Stolboushkina EA]]

9xtc: Difference between revisions

Latest revision as of 06:34, 8 April 2026

E.coli delta lepA 30S ribosomal subunit class C, body domain

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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