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| ==Promiscuous behavior of proteins in archaeal ribosomes revealed by cryo-EM: implications for evolution of eukaryotic ribosomes== | | ==Promiscuous behavior of proteins in archaeal ribosomes revealed by cryo-EM: implications for evolution of eukaryotic ribosomes== |
| <StructureSection load='4v6u' size='340' side='right'caption='[[4v6u]], [[Resolution|resolution]] 6.60Å' scene=''> | | <SX load='4v6u' size='340' side='right' viewer='molstar' caption='[[4v6u]], [[Resolution|resolution]] 6.60Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4v6u]] is a 72 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j20 3j20], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j21 3j21] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j2l 3j2l]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V6U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V6U FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4v6u]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j20 3j20], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j21 3j21] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j2l 3j2l]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V6U FirstGlance]. <br> |
| </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr> | | </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=4v6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v6u OCA], [https://pdbe.org/4v6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v6u RCSB], [https://www.ebi.ac.uk/pdbsum/4v6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v6u ProSAT]</span></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=4v6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v6u OCA], [http://pdbe.org/4v6u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v6u RCSB], [http://www.ebi.ac.uk/pdbsum/4v6u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v6u ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RL3_PYRFU RL3_PYRFU]] 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. [[http://www.uniprot.org/uniprot/RL18_PYRFU RL18_PYRFU]] 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. [[http://www.uniprot.org/uniprot/RS14Z_PYRFU RS14Z_PYRFU]] Binds 16S rRNA, required for the assembly of 30S particles. [[http://www.uniprot.org/uniprot/RS5_PYRFU RS5_PYRFU]] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] [[http://www.uniprot.org/uniprot/RL7A_PYRFU RL7A_PYRFU]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). [[http://www.uniprot.org/uniprot/RS4_PYRFU RS4_PYRFU]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. [[http://www.uniprot.org/uniprot/RL15_PYRFU RL15_PYRFU]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL14_PYRFU RL14_PYRFU]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [[http://www.uniprot.org/uniprot/RS10_PYRFU RS10_PYRFU]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL24E_PYRFU RL24E_PYRFU]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL37_PYRFU RL37_PYRFU]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RS12_PYRFU RS12_PYRFU]] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits. [[http://www.uniprot.org/uniprot/RL2_PYRFU RL2_PYRFU]] 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. [[http://www.uniprot.org/uniprot/RL22_PYRFU RL22_PYRFU]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. 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. [[http://www.uniprot.org/uniprot/RL11_PYRFU RL11_PYRFU]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. [[http://www.uniprot.org/uniprot/RL37A_PYRFU RL37A_PYRFU]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL10_PYRFU RL10_PYRFU]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [[http://www.uniprot.org/uniprot/RL6_PYRFU RL6_PYRFU]] 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. [[http://www.uniprot.org/uniprot/RS13_PYRFU RS13_PYRFU]] 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. [[http://www.uniprot.org/uniprot/Q8U0T4_PYRFU Q8U0T4_PYRFU]] May be involved in maturation of the 30S ribosomal subunit.[HAMAP-Rule:MF_01474] [[http://www.uniprot.org/uniprot/RS7_PYRFU RS7_PYRFU]] 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. [[http://www.uniprot.org/uniprot/RL5_PYRFU RL5_PYRFU]] 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. May contact the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. [[http://www.uniprot.org/uniprot/RS11_PYRFU RS11_PYRFU]] Located on the platform of the 30S subunit. [[http://www.uniprot.org/uniprot/RL19E_PYRFU RL19E_PYRFU]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL4_PYRFU RL4_PYRFU]] 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. Forms part of the polypeptide exit tunnel. [[http://www.uniprot.org/uniprot/RL23_PYRFU RL23_PYRFU]] Binds to 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL1_PYRFU RL1_PYRFU]] Binds directly to 23S rRNA. Probably involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of its operon by binding to its mRNA. [[http://www.uniprot.org/uniprot/RS19_PYRFU RS19_PYRFU]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS3_PYRFU RS3_PYRFU]] Binds the lower part of the 30S subunit head. [[http://www.uniprot.org/uniprot/RS8_PYRFU RS8_PYRFU]] 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. [[http://www.uniprot.org/uniprot/RL44E_PYRFU RL44E_PYRFU]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL13_PYRFU RL13_PYRFU]] 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. [[http://www.uniprot.org/uniprot/RS17_PYRFU RS17_PYRFU]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL24_PYRFU RL24_PYRFU]] 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.[HAMAP-Rule:MF_01326] Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326] | | [https://www.uniprot.org/uniprot/RS15_PYRFU RS15_PYRFU] |
| <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </SX> |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Pyrococcus furiosus]] | | [[Category: Pyrococcus furiosus DSM 3638]] |
| [[Category: Anger, A M]] | | [[Category: Anger AM]] |
| [[Category: Armache, J P]] | | [[Category: Armache J-P]] |
| [[Category: Arnold, G J]] | | [[Category: Arnold GJ]] |
| [[Category: Beckmann, R]] | | [[Category: Beckmann R]] |
| [[Category: Berninghausen, O]] | | [[Category: Berninghausen O]] |
| [[Category: Frankenberg, S]] | | [[Category: Frankenberg S]] |
| [[Category: Froehlich, T]] | | [[Category: Froehlich T]] |
| [[Category: Marquez, V]] | | [[Category: Marquez V]] |
| [[Category: Thomm, M]] | | [[Category: Thomm M]] |
| [[Category: Villa, E]] | | [[Category: Villa E]] |
| [[Category: Wilson, D N]] | | [[Category: Wilson DN]] |
| [[Category: Archaea]]
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| [[Category: Archaeal]]
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| [[Category: Kink-turn]]
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| [[Category: Protein synthesis]]
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| [[Category: Ribosomal]]
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| [[Category: Ribosome]]
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| [[Category: Rna]]
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