4v6u

Promiscuous behavior of proteins in archaeal ribosomes revealed by cryo-EM: implications for evolution of eukaryotic ribosomes

spinqualitylabelsall models 4v6u, resolution 6.60Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4v6u is a 72 chain structure with sequence from Pyrococcus furiosus. This structure supersedes the now removed PDB entries and 3j2l. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. NonStd Res: UNK Related: 3j20, 3j21, 3j2l Resources: FirstGlance, OCA, RCSB, PDBsum Function [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. [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. [RS14Z_PYRFU] Binds 16S rRNA, required for the assembly of 30S particles. [RS5_PYRFU] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] [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). [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. [RL15_PYRFU] Binds to the 23S rRNA. [RL14_PYRFU] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [RS10_PYRFU] Involved in the binding of tRNA to the ribosomes. [RL24E_PYRFU] Binds to the 23S rRNA. [RL37_PYRFU] Binds to the 23S rRNA. [RS12_PYRFU] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits. [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. [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. [RL11_PYRFU] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. [RL37A_PYRFU] Binds to the 23S rRNA. [RL10_PYRFU] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [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. [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. [Q8U0T4_PYRFU] May be involved in maturation of the 30S ribosomal subunit.[HAMAP-Rule:MF_01474] [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. [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. [RS11_PYRFU] Located on the platform of the 30S subunit. [RL19E_PYRFU] Binds to the 23S rRNA.[HAMAP-Rule:MF_01475] [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. [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] [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. [RS19_PYRFU] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [RS3_PYRFU] Binds the lower part of the 30S subunit head. [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. [RL44E_PYRFU] Binds to the 23S rRNA. [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. [RS17_PYRFU] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [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] Publication Abstract from PubMed In all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. Molecular models have been reported for complete bacterial 70S and eukaryotic 80S ribosomes; however, only molecular models of large 50S subunits have been reported for archaea. Here, we present a complete molecular model for the Pyrococcus furiosus 70S ribosome based on a 6.6 A cryo-electron microscopy map. Moreover, we have determined cryo-electron microscopy reconstructions of the Euryarchaeota Methanococcus igneus and Thermococcus kodakaraensis 70S ribosomes and Crenarchaeota Staphylothermus marinus 50S subunit. Examination of these structures reveals a surprising promiscuous behavior of archaeal ribosomal proteins: We observe intersubunit promiscuity of S24e and L8e (L7ae), the latter binding to the head of the small subunit, analogous to S12e in eukaryotes. Moreover, L8e and L14e exhibit intrasubunit promiscuity, being present in two copies per archaeal 50S subunit, with the additional binding site of L14e analogous to the related eukaryotic r-protein L27e. Collectively, these findings suggest insights into the evolution of eukaryotic ribosomal proteins through increased copy number and binding site promiscuity. Promiscuous behaviour of archaeal ribosomal proteins: Implications for eukaryotic ribosome evolution.,Armache JP, Anger AM, Marquez V, Franckenberg S, Frohlich T, Villa E, Berninghausen O, Thomm M, Arnold GJ, Beckmann R, Wilson DN Nucleic Acids Res. 2012 Dec 6. PMID:23222135 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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