2r1g: Difference between revisions

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<SX load='2r1g' size='340' side='right' viewer='molstar' caption='[[2r1g]], [[Resolution|resolution]] 12.50&Aring;' scene=''>
<SX load='2r1g' size='340' side='right' viewer='molstar' caption='[[2r1g]], [[Resolution|resolution]] 12.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2r1g]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1G FirstGlance]. <br>
<table><tr><td colspan='2'>[[2r1g]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1G FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j5e|1j5e]], [[2r1c|2r1c]], [[2dyj|2dyj]]</div></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]] 12.5&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpsM, rps13 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2]), rpsI, rps9 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2]), rpsL, rps12 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=2r1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1g OCA], [https://pdbe.org/2r1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1g RCSB], [https://www.ebi.ac.uk/pdbsum/2r1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1g ProSAT]</span></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=2r1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1g OCA], [https://pdbe.org/2r1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1g RCSB], [https://www.ebi.ac.uk/pdbsum/2r1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1g ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://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] [[https://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[https://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity).  
[https://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2r1g 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=2r1g ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock.
Structural aspects of RbfA action during small ribosomal subunit assembly.,Datta PP, Wilson DN, Kawazoe M, Swami NK, Kaminishi T, Sharma MR, Booth TM, Takemoto C, Fucini P, Yokoyama S, Agrawal RK Mol Cell. 2007 Nov 9;28(3):434-45. PMID:17996707<ref>PMID:17996707</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2r1g" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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*[[Ribosomal protein S13|Ribosomal protein S13]]
*[[Ribosomal protein S13|Ribosomal protein S13]]
*[[Ribosomal protein S9|Ribosomal protein S9]]
*[[Ribosomal protein S9|Ribosomal protein S9]]
== References ==
<references/>
__TOC__
__TOC__
</SX>
</SX>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Thet2]]
[[Category: Synthetic construct]]
[[Category: Agrawal, R K]]
[[Category: Thermus thermophilus HB27]]
[[Category: Booth, T M]]
[[Category: Agrawal RK]]
[[Category: Datta, P P]]
[[Category: Booth TM]]
[[Category: Fucini, P]]
[[Category: Datta PP]]
[[Category: Kaminishi, T]]
[[Category: Fucini P]]
[[Category: Kawazoe, M]]
[[Category: Kaminishi T]]
[[Category: Sharma, M R]]
[[Category: Kawazoe M]]
[[Category: Swami, N K]]
[[Category: Sharma MR]]
[[Category: Takemoto, C]]
[[Category: Swami NK]]
[[Category: Wilson, D N]]
[[Category: Takemoto C]]
[[Category: Yokoyama, S]]
[[Category: Wilson DN]]
[[Category: 30s ribosome maturation protein rbfa]]
[[Category: Yokoyama S]]
[[Category: 30s-rbfa complex]]
[[Category: Antibiotic resistance]]
[[Category: Cold shock response protein rbfa]]
[[Category: Rbfa binding site on the 30]]
[[Category: Ribonucleoprotein]]
[[Category: Ribosomal protein]]
[[Category: Ribosomal protein-rna complex]]
[[Category: Rna-binding]]
[[Category: Rrna-binding]]
[[Category: Trna-binding]]

Latest revision as of 16:54, 13 March 2024

Coordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complexCoordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complex

2r1g, resolution 12.50Å

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