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| | <StructureSection load='4xej' size='340' side='right'caption='[[4xej]], [[Resolution|resolution]] 3.80Å' scene=''> | | <StructureSection load='4xej' size='340' side='right'caption='[[4xej]], [[Resolution|resolution]] 3.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4xej]] is a 106 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XEJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4xej]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XEJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8Å</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=4xej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xej OCA], [http://pdbe.org/4xej PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xej RCSB], [http://www.ebi.ac.uk/pdbsum/4xej PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xej ProSAT]</span></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> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xej OCA], [https://pdbe.org/4xej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xej RCSB], [https://www.ebi.ac.uk/pdbsum/4xej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xej ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity). [[http://www.uniprot.org/uniprot/RL11_THET2 RL11_THET2]] This protein binds directly to 23S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RL3_THET2 RL3_THET2]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). [[http://www.uniprot.org/uniprot/RL22_THET2 RL22_THET2]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL2_THET2 RL2_THET2]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL23_THET2 RL23_THET2]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RL21_THET2 RL21_THET2]] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). [[http://www.uniprot.org/uniprot/RS17_THET2 RS17_THET2]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RL34_THET8 RL34_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00391] [[http://www.uniprot.org/uniprot/RL32_THET2 RL32_THET2]] Found on the solvent side of the large subunit (By similarity). [[http://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). [[http://www.uniprot.org/uniprot/RL19_THET2 RL19_THET2]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site (By similarity). [[http://www.uniprot.org/uniprot/RL25_THET2 RL25_THET2]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance (By similarity). [[http://www.uniprot.org/uniprot/RL31_THET2 RL31_THET2]] Binds the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL15_THET2 RL15_THET2]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RL16_THET2 RL16_THET2]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] 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). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RL18_THET2 RL18_THET2]] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RL9_THET2 RL9_THET2]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). 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). [[http://www.uniprot.org/uniprot/RL4_THET2 RL4_THET2]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). Forms part of the polypeptide exit tunnel (By similarity). [[http://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). [[http://www.uniprot.org/uniprot/RL14_THET2 RL14_THET2]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, 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). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RL20_THET2 RL20_THET2]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity). [[http://www.uniprot.org/uniprot/RL13_THET2 RL13_THET2]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly (By similarity). [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RL5_THET2 RL5_THET2]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 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, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] 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). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RL24_THET2 RL24_THET2]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity). [[http://www.uniprot.org/uniprot/RL6_THET2 RL6_THET2]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center (By similarity).
| + | [https://www.uniprot.org/uniprot/RL2_THET2 RL2_THET2] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4xej" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4xej" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]] |
| | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thermus thermophilus hb27]] | + | [[Category: Thermus thermophilus HB27]] |
| - | [[Category: Donohue, J P]] | + | [[Category: Donohue JP]] |
| - | [[Category: Korostelev, A]] | + | [[Category: Korostelev A]] |
| - | [[Category: Noller, H F]] | + | [[Category: Noller HF]] |
| - | [[Category: Zhu, J]] | + | [[Category: Zhu J]] |
| - | [[Category: Bacterial initiation]]
| + | |
| - | [[Category: Internal ribosome entry site]]
| + | |
| - | [[Category: Ire]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| Structural highlights
Function
RL2_THET2 One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).
Publication Abstract from PubMed
The central dogma of gene expression (DNA to RNA to protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive. However, the core structures and conformational dynamics of ribosomes that are responsible for the translation steps that take place after initiation are ancient and conserved across the domains of life. We wanted to explore whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 A resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by transfer RNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA, but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence and provides an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.
Initiation of translation in bacteria by a structured eukaryotic IRES RNA.,Colussi TM, Costantino DA, Zhu J, Donohue JP, Korostelev AA, Jaafar ZA, Plank TD, Noller HF, Kieft JS Nature. 2015 Feb 4. doi: 10.1038/nature14219. PMID:25652826[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Colussi TM, Costantino DA, Zhu J, Donohue JP, Korostelev AA, Jaafar ZA, Plank TD, Noller HF, Kieft JS. Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature. 2015 Feb 4. doi: 10.1038/nature14219. PMID:25652826 doi:http://dx.doi.org/10.1038/nature14219
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