2e5l

<table><tr><td colspan='2'>[[2e5l]] is a 23 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=2E5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E5L FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>

[[https://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[https://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[https://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[https://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[https://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[https://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[https://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] 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.[HAMAP-Rule:MF_00403_B] [[https://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[https://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B] [[https://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] [[https://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[https://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[https://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[https://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[https://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[https://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_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/RS18_THETH RS18_THETH]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[https://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B]

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== Publication Abstract from PubMed ==

In the initiation phase of bacterial translation, the 30S ribosomal subunit captures mRNA in preparation for binding with initiator tRNA. The purine-rich Shine-Dalgarno (SD) sequence, in the 5' untranslated region of the mRNA, anchors the 30S subunit near the start codon, via base pairing with an anti-SD (aSD) sequence at the 3' terminus of 16S rRNA. Here, we present the 3.3 A crystal structure of the Thermus thermophilus 30S subunit bound with an mRNA mimic. The duplex formed by the SD and aSD sequences is snugly docked in a "chamber" between the head and platform domains, demonstrating how the 30S subunit captures and stabilizes the otherwise labile SD helix. This location of the SD helix is suitable for the placement of the start codon AUG in the immediate vicinity of the mRNA channel, in agreement with reported crosslinks between the second position of the start codon and G1530 of 16S rRNA.

A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.,Kaminishi T, Wilson DN, Takemoto C, Harms JM, Kawazoe M, Schluenzen F, Hanawa-Suetsugu K, Shirouzu M, Fucini P, Yokoyama S Structure. 2007 Mar;15(3):289-97. PMID:17355865<ref>PMID:17355865</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

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<div class="pdbe-citations 2e5l" style="background-color:#fffaf0;"></div>

*[[Ribosome 3D structures|Ribosome 3D structures]]

== References ==

<references/>

[[Category: Fucini, P]]

[[Category: Hanawa-Suetsugu, K]]

[[Category: Harms, J M]]

[[Category: Kaminishi, T]]

[[Category: Kawazoe, M]]

[[Category: Structural genomic]]

[[Category: Schluenzen, F]]

[[Category: Shirouzu, M]]

[[Category: Takemoto, C]]

[[Category: Wilson, D N]]

[[Category: Yokoyama, S]]

[[Category: Translation initiation]]