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| - | {{Large structure}}
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| | ==Structure of the large subunit of the chloro-ribosome== | | ==Structure of the large subunit of the chloro-ribosome== |
| - | <StructureSection load='5h1s' size='340' side='right' caption='[[5h1s]], [[Resolution|resolution]] 3.50Å' scene=''> | + | <SX load='5h1s' size='340' side='right' viewer='molstar' caption='[[5h1s]], [[Resolution|resolution]] 3.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5h1s]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H1S FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5h1s]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H1S FirstGlance]. <br> |
| - | </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=5h1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1s OCA], [http://pdbe.org/5h1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h1s RCSB], [http://www.ebi.ac.uk/pdbsum/5h1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1s ProSAT]</span></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]] 3.5Å</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=5h1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1s OCA], [https://pdbe.org/5h1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h1s RCSB], [https://www.ebi.ac.uk/pdbsum/5h1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1s ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | {{Large structure}} | |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RK4_SPIOL RK4_SPIOL]] Probably binds the 23S rRNA (By similarity). This protein (expressed without the transit peptide) is able to provoke transcription termination from the spinach chloroplast rDNA operon and the E.coli S10 operon in vitro. [[http://www.uniprot.org/uniprot/RK5_SPIOL RK5_SPIOL]] Binds 5S rRNA, forms part of the central protuberance of the 50S subunit (By similarity). [[http://www.uniprot.org/uniprot/RK23_SPIOL RK23_SPIOL]] Binds to 23S rRNA (By similarity). Located at the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RK19_SPIOL RK19_SPIOL]] Located at the 30S-50S ribosomal subunit interface and binds directly to 23S ribosomal RNA (By similarity).[:] [[http://www.uniprot.org/uniprot/RK20_SPIOL RK20_SPIOL]] 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).[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RK34_SPIOL RK34_SPIOL]] This protein binds directly to 23S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RK22_SPIOL RK22_SPIOL]] This protein binds specifically to 23S rRNA (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). Binds an erythromycin derivative added to the 50S subunit. [[http://www.uniprot.org/uniprot/RK21_SPIOL RK21_SPIOL]] This protein binds to 23S ribosomal RNA in the presence of protein L20 (By similarity). [[http://www.uniprot.org/uniprot/RK24_SPIOL RK24_SPIOL]] 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). Located at the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RK14_SPIOL RK14_SPIOL]] Binds to 23S rRNA (By similarity). | + | [https://www.uniprot.org/uniprot/RK13_SPIOL RK13_SPIOL] |
| | <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 5h1s" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5h1s" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| - | </StructureSection> | + | </SX> |
| | + | [[Category: Large Structures]] |
| | [[Category: Spinacia oleracea]] | | [[Category: Spinacia oleracea]] |
| - | [[Category: Ahmed, T]] | + | [[Category: Ahmed T]] |
| - | [[Category: Bhushan, S]] | + | [[Category: Bhushan S]] |
| - | [[Category: Yin, Z]] | + | [[Category: Yin Z]] |
| - | [[Category: Chloro-ribosome]]
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| - | [[Category: Cryo-em]]
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| - | [[Category: Ribosome]]
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| Structural highlights
Function
RK13_SPIOL
Publication Abstract from PubMed
Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 A. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features.
Cryo-EM structure of the large subunit of the spinach chloroplast ribosome.,Ahmed T, Yin Z, Bhushan S Sci Rep. 2016 Oct 20;6:35793. doi: 10.1038/srep35793. PMID:27762343[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ahmed T, Yin Z, Bhushan S. Cryo-EM structure of the large subunit of the spinach chloroplast ribosome. Sci Rep. 2016 Oct 20;6:35793. doi: 10.1038/srep35793. PMID:27762343 doi:http://dx.doi.org/10.1038/srep35793
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